1-159722915-A-G

Variant names:

• chr1-159722915-A-G
• rs2794517
• ENST00000751816.1:n.108-3612A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751816.1(ENSG00000297913):​n.108-3612A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,062 control chromosomes in the GnomAD database, including 45,874 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 0.77 (45874 hom., cov: 31)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

ENSG00000297913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297913	ENST00000751816.1	n.108-3612A>G		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.110-3612A>G		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.63-3612A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117636 AN: 151944 Hom.: 45822 Cov.: 31

Gnomad AFR AF: 0.854

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.774 AC: 117748 AN: 152062 Hom.: 45874 Cov.: 31 AF XY: 0.776 AC XY: 57683 AN XY: 74326

African (AFR) AF: 0.854 AC: 35441 AN: 41484

American (AMR) AF: 0.798 AC: 12190 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2877 AN: 3468

East Asian (EAS) AF: 0.824 AC: 4257 AN: 5164

South Asian (SAS) AF: 0.668 AC: 3219 AN: 4820

European-Finnish (FIN) AF: 0.801 AC: 8467 AN: 10570

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48851 AN: 67972

Other (OTH) AF: 0.781 AC: 1647 AN: 2108

Alfa AF: 0.757 Hom.: 5445

Bravo AF: 0.779

Asia WGS AF: 0.741 AC: 2580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2794517; hg19: chr1-159692705;