Genetic Variant AHSA1:c.792+60T>C (chr14-77468244-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012111.3(AHSA1):c.792+60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,250,920 control chromosomes in the GnomAD database, including 11,278 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1107 hom., cov: 29)

Exomes 𝑓: 0.13 ( 10171 hom. )

Consequence

AHSA1
NM_012111.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.156

Publications

7 publications found

Variant links:

Genes affected

AHSA1 (HGNC:1189): (activator of HSP90 ATPase activity 1) Enables ATPase activator activity; Hsp90 protein binding activity; and chaperone binding activity. Involved in positive regulation of ATPase activity. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

AHSA1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012111.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHSA1	NM_012111.3	MANE Select	c.792+60T>C		intron	N/A	NP_036243.1
	AHSA1	NM_001321441.2		c.387+60T>C		intron	N/A	NP_001308370.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
AHSA1	ENST00000216479.8	TSL:1 MANE Select	c.792+60T>C	intron	N/A	ENSP00000216479.3
AHSA1	ENST00000553374.5	TSL:2	c.*39T>C	3_prime_UTR	Exon 6 of 6	ENSP00000451475.1
AHSA1	ENST00000535854.6	TSL:2	c.792+60T>C	intron	N/A	ENSP00000440108.2

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16673

AN:

150882

Hom.:

1107

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0666

Gnomad AMI

AF:

0.0385

Gnomad AMR

AF:

0.116

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.0195

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.290

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.146

GnomAD2 exomes

AF:

0.126

AC:

15767

AN:

125222

AF XY:

0.133

show subpopulations

Gnomad AFR exome

AF:

0.0653

Gnomad AMR exome

AF:

0.0932

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.0177

Gnomad FIN exome

AF:

0.132

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.146

GnomAD4 exome

AF:

0.130

AC:

142495

AN:

1099922

Hom.:

10171

Cov.:

AF XY:

0.132

AC XY:

73176

AN XY:

553312

show subpopulations

African (AFR)

AF:

0.0655

AC:

1586

AN:

24202

American (AMR)

AF:

0.0887

AC:

2263

AN:

25524

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

2869

AN:

21770

East Asian (EAS)

AF:

0.0134

AC:

461

AN:

34282

South Asian (SAS)

AF:

0.211

AC:

14336

AN:

68072

European-Finnish (FIN)

AF:

0.128

AC:

6267

AN:

48822

Middle Eastern (MID)

AF:

0.250

AC:

1250

AN:

4992

European-Non Finnish (NFE)

AF:

0.130

AC:

107283

AN:

824654

Other (OTH)

AF:

0.130

AC:

6180

AN:

47604

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

6242

12484

18727

24969

31211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3534

7068

10602

14136

17670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.110

AC:

16671

AN:

150998

Hom.:

1107

Cov.:

AF XY:

0.111

AC XY:

8225

AN XY:

73770

show subpopulations

African (AFR)

AF:

0.0665

AC:

2758

AN:

41460

American (AMR)

AF:

0.116

AC:

1700

AN:

14698

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

421

AN:

3452

East Asian (EAS)

AF:

0.0193

AC:

100

AN:

5170

South Asian (SAS)

AF:

0.201

AC:

954

AN:

4744

European-Finnish (FIN)

AF:

0.124

AC:

1307

AN:

10540

Middle Eastern (MID)

AF:

0.302

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.133

AC:

9005

AN:

67646

Other (OTH)

AF:

0.145

AC:

304

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

733

1466

2200

2933

3666

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

384

576

768

960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.132

Hom.:

2485

Bravo

AF:

0.105

Asia WGS

AF:

0.106

AC:

372

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

(source)

DANN

Benign

0.50

PhyloP100

-0.16

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over