Genetic Variant AHI1-DT:n.230+8273C>T (chr6-135698009-C-T) – 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+8273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,076 control chromosomes in the GnomAD database, including 5,841 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 0.26 ( 5841 hom., cov: 32)

Consequence

AHI1-DT
ENST00000579944.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.229

Publications

4 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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 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+8273C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AHI1-DT	ENST00000579944.1 link	n.230+8273C>T	intron_variant	Intron 2 of 2	2
AHI1-DT	ENST00000655302.1 link	n.543+8273C>T	intron_variant	Intron 4 of 6
AHI1-DT	ENST00000685995.1 link	n.781+8273C>T	intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39732

AN:

151958

Hom.:

5832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.359

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.402

Gnomad SAS

AF:

0.413

Gnomad FIN

AF:

0.194

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.258

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

GnomAD4 genome

AF:

0.261

AC:

39751

AN:

152076

Hom.:

5841

Cov.:

AF XY:

0.259

AC XY:

19266

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.128

AC:

5332

AN:

41504

American (AMR)

AF:

0.307

AC:

4693

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1092

AN:

3472

East Asian (EAS)

AF:

0.403

AC:

2075

AN:

5148

South Asian (SAS)

AF:

0.413

AC:

1991

AN:

4818

European-Finnish (FIN)

AF:

0.194

AC:

2056

AN:

10582

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.317

AC:

21568

AN:

67968

Other (OTH)

AF:

0.259

AC:

546

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1469

2938

4406

5875

7344

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.298

Hom.:

11903

Bravo

AF:

0.260

Asia WGS

AF:

0.354

AC:

1228

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.1

(source)

DANN

Benign

0.61

PhyloP100

0.23

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