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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810862.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305424	ENST00000810862.1		n.391-3317C>G		intron	N/A
	ENSG00000305424	ENST00000810863.1		n.440-3317C>G		intron	N/A
	ENSG00000305424	ENST00000810864.1		n.205-3317C>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2914161;

hg19: chr5-113023439;