rs2167176

Variant names:

• chr3-35355995-A-G
• rs2167176
• ENST00000797381.1:n.388+37877T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-35355995-A-G
• chr3-35355995-A-T

Variant summary

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

The ENST00000797381.1(ENSG00000289420):​n.388+37877T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,656 control chromosomes in the GnomAD database, including 30,965 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 0.62 (30965 hom., cov: 31)
• Consequence: ENSG00000289420 ENST00000797381.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 4 publications found

Genes affected

ENSG00000289420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928135	NR_110817.1	n.152+37877T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289420	ENST00000797381.1	n.388+37877T>C		intron_variant	Intron 3 of 5
ENSG00000289420	ENST00000797382.1	n.388+37877T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94479 AN: 151538 Hom.: 30903 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.624 AC: 94593 AN: 151656 Hom.: 30965 Cov.: 31 AF XY: 0.622 AC XY: 46089 AN XY: 74102

African (AFR) AF: 0.818 AC: 33887 AN: 41410

American (AMR) AF: 0.647 AC: 9840 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2048 AN: 3458

East Asian (EAS) AF: 0.542 AC: 2768 AN: 5110

South Asian (SAS) AF: 0.753 AC: 3629 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4712 AN: 10550

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35679 AN: 67796

Other (OTH) AF: 0.633 AC: 1334 AN: 2106

Alfa AF: 0.575 Hom.: 63697

Bravo AF: 0.645

Asia WGS AF: 0.700 AC: 2432 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	2.2
DANN	Benign	0.36
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2167176; hg19: chr3-35397487;