rs2914161

Variant names:

• chr5-113687742-C-G
• rs2914161
• ENST00000810862.1:n.391-3317C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-113687742-C-G
• chr5-113687742-C-T

Variant summary

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

The ENST00000810862.1(ENSG00000305424):​n.391-3317C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,016 control chromosomes in the GnomAD database, including 17,547 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 0.44 (17547 hom., cov: 33)
• Consequence: ENSG00000305424 ENST00000810862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 1 publications found

Genes affected

ENSG00000305424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986441	XR_001742841.1	n.60-3317C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305424	ENST00000810862.1	n.391-3317C>G		intron_variant	Intron 3 of 4
ENSG00000305424	ENST00000810863.1	n.440-3317C>G		intron_variant	Intron 2 of 5
ENSG00000305424	ENST00000810864.1	n.205-3317C>G		intron_variant	Intron 2 of 3
ENSG00000305424	ENST00000810865.1	n.160-3317C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66296 AN: 151898 Hom.: 17553 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.436 AC: 66287 AN: 152016 Hom.: 17547 Cov.: 33 AF XY: 0.447 AC XY: 33234 AN XY: 74310

African (AFR) AF: 0.119 AC: 4910 AN: 41400

American (AMR) AF: 0.622 AC: 9491 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2006 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3594 AN: 5168

South Asian (SAS) AF: 0.662 AC: 3196 AN: 4830

European-Finnish (FIN) AF: 0.547 AC: 5787 AN: 10578

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35775 AN: 67984

Other (OTH) AF: 0.505 AC: 1067 AN: 2114

Alfa AF: 0.457 Hom.: 2215

Bravo AF: 0.427

Asia WGS AF: 0.602 AC: 2092 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2914161; hg19: chr5-113023439;