dbSNP rs4896180: AHI1-DT:n.669-21154T>C (chr6-135788693-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 ENST00000655302.1(AHI1-DT):n.669-21154T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0745 in 152,230 control chromosomes in the GnomAD database, including 687 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 0.075 ( 687 hom., cov: 32)

Consequence

AHI1-DT
ENST00000655302.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215

Publications

1 publications found

Variant links:

COSMIC-nc: COSV69427788

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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.669-21154T>C	intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1 link	n.821+11916T>C	intron_variant	Intron 6 of 7
AHI1-DT	ENST00000690403.2 link	n.508-21154T>C	intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.0744

AC:

11317

AN:

152112

Hom.:

685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0508

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.0463

Gnomad SAS

AF:

0.0656

Gnomad FIN

AF:

0.0226

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0366

Gnomad OTH

AF:

0.0635

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

GnomAD4 genome

AF:

0.0745

AC:

11342

AN:

152230

Hom.:

687

Cov.:

AF XY:

0.0719

AC XY:

5353

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.171

AC:

7095

AN:

41542

American (AMR)

AF:

0.0506

AC:

772

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3468

East Asian (EAS)

AF:

0.0462

AC:

240

AN:

5192

South Asian (SAS)

AF:

0.0659

AC:

318

AN:

4826

European-Finnish (FIN)

AF:

0.0226

AC:

240

AN:

10624

Middle Eastern (MID)

AF:

0.0171

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0366

AC:

2487

AN:

67988

Other (OTH)

AF:

0.0652

AC:

138

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

510

1019

1529

2038

2548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0495

Hom.:

847

Bravo

AF:

0.0824

Asia WGS

AF:

0.0690

AC:

239

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.5

(source)

DANN

Benign

0.76

PhyloP100

-0.21

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