dbSNP rs9483869: AHI1-DT:n.230+12040T>C (chr6-135701776-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -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

Variant links:

Genes affected

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

AHI1-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.0469

Gnomad4 ASJ

AF:

0.0340

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0284

Gnomad4 FIN

AF:

0.00283

Gnomad4 NFE

AF:

0.0109

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.0540

Hom.:

324

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

DANN

Benign

0.29

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over