Genetic Variant AHI1-DT:n.230+12040T>C (chr6-135701776-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 ENST00000579944.1(AHI1-DT):n.230+12040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,096 control chromosomes in the GnomAD database, including 2,087 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 0.099 ( 2087 hom., cov: 32)

Consequence

AHI1-DT
ENST00000579944.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

2 publications found

Variant links:

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

AHI1-DT links:

Genome browser will be placed here

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=-0.99).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_152842.1 link	n.648+12040T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AHI1-DT	ENST00000579944.1 link	n.230+12040T>C	intron_variant	Intron 2 of 2	2
AHI1-DT	ENST00000655302.1 link	n.543+12040T>C	intron_variant	Intron 4 of 6
AHI1-DT	ENST00000685995.1 link	n.781+12040T>C	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.0986

AC:

14979

AN:

151978

Hom.:

2070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.0471

Gnomad ASJ

AF:

0.0340

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0284

Gnomad FIN

AF:

0.00283

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0109

Gnomad OTH

AF:

0.0837

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0989

AC:

15043

AN:

152096

Hom.:

2087

Cov.:

AF XY:

0.0962

AC XY:

7151

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.316

AC:

13074

AN:

41416

American (AMR)

AF:

0.0469

AC:

717

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0340

AC:

118

AN:

3470

East Asian (EAS)

AF:

0.000965

AC:

AN:

5182

South Asian (SAS)

AF:

0.0284

AC:

137

AN:

4824

European-Finnish (FIN)

AF:

0.00283

AC:

AN:

10606

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0109

AC:

742

AN:

68006

Other (OTH)

AF:

0.0866

AC:

183

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

542

1085

1627

2170

2712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0592

Hom.:

416

Bravo

AF:

0.112

Asia WGS

AF:

0.0510

AC:

176

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.42

(source)

DANN

Benign

0.29

PhyloP100

-1.7

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over