Genetic Variant AHI1-DT:n.668+15864G>A (chr6-135731810-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655302.1(AHI1-DT):n.668+15864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,948 control chromosomes in the GnomAD database, including 5,884 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 ( 5884 hom., cov: 32)

Consequence

AHI1-DT
ENST00000655302.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.129

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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
AHI1-DT	ENST00000655302.1 link	n.668+15864G>A	intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1 link	n.781+42074G>A	intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.2 link	n.507+42074G>A	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39792

AN:

151828

Hom.:

5870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.424

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.304

Gnomad OTH

AF:

0.265

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

GnomAD4 genome

AF:

0.262

AC:

39832

AN:

151948

Hom.:

5884

Cov.:

AF XY:

0.259

AC XY:

19263

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.146

AC:

6045

AN:

41446

American (AMR)

AF:

0.326

AC:

4973

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1069

AN:

3470

East Asian (EAS)

AF:

0.457

AC:

2365

AN:

5170

South Asian (SAS)

AF:

0.425

AC:

2048

AN:

4820

European-Finnish (FIN)

AF:

0.163

AC:

1710

AN:

10520

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.304

AC:

20687

AN:

67952

Other (OTH)

AF:

0.268

AC:

566

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1470

2941

4411

5882

7352

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:

0.269

Hom.:

767

Bravo

AF:

0.268

Asia WGS

AF:

0.400

AC:

1383

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

2.9

(source)

DANN

Benign

0.65

PhyloP100

0.13

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