Variant rs2273069 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NR_152842.1(AHI1-DT):n.572A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00822 in 151,876 control chromosomes in the GnomAD database, including 15 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 0.0082 ( 15 hom., cov: 32)

Exomes 𝑓: 0.015 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AHI1-DT
NR_152842.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

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=-0.91).

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00822 (1248/151876) while in subpopulation SAS AF= 0.0415 (200/4814). AF 95% confidence interval is 0.0368. There are 15 homozygotes in gnomad4. There are 652 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
AHI1-DT	NR_152842.1 linkuse as main transcript	n.572A>C	non_coding_transcript_exon_variant	5/6
AHI1-DT	NR_026805.1 linkuse as main transcript	n.458A>C	non_coding_transcript_exon_variant	4/4
AHI1-DT	NR_152844.1 linkuse as main transcript	n.572A>C	non_coding_transcript_exon_variant	5/5
AHI1-DT	NR_152845.1 linkuse as main transcript	n.696A>C	non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1 linkuse as main transcript	n.405A>C		non_coding_transcript_exon_variant	4/8

Frequencies

GnomAD3 genomes

AF:

0.00822

AC:

1248

AN:

151758

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00174

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00643

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.00213

Gnomad SAS

AF:

0.0415

Gnomad FIN

AF:

0.00730

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00670

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0147

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0227

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0185

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00822

AC:

1248

AN:

151876

Hom.:

Cov.:

AF XY:

0.00879

AC XY:

652

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.00174

Gnomad4 AMR

AF:

0.00643

Gnomad4 ASJ

AF:

0.0196

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.0415

Gnomad4 FIN

AF:

0.00730

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00663

Alfa

AF:

0.00189

Hom.:

295

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.17

DANN

Benign

0.59

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