rs4463179

Variant names:

• chr5-13505322-G-A
• rs4463179
• XR_001742606.2:n.502+71270C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-13505322-G-A
• chr5-13505322-G-C

Variant summary

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

The XR_001742606.2(LOC105374660):​n.502+71270C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 151,806 control chromosomes in the GnomAD database, including 2,891 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 0.17 (2891 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 9 publications found

Genes affected

LOC105374660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25618 AN: 151688 Hom.: 2875 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0840

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0975

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.169 AC: 25654 AN: 151806 Hom.: 2891 Cov.: 32 AF XY: 0.169 AC XY: 12564 AN XY: 74128

African (AFR) AF: 0.292 AC: 12064 AN: 41358

American (AMR) AF: 0.145 AC: 2213 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0840 AC: 291 AN: 3464

East Asian (EAS) AF: 0.358 AC: 1846 AN: 5152

South Asian (SAS) AF: 0.203 AC: 977 AN: 4808

European-Finnish (FIN) AF: 0.0975 AC: 1022 AN: 10486

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0989 AC: 6721 AN: 67960

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.124 Hom.: 2855

Bravo AF: 0.178

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.46
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4463179; hg19: chr5-13505432; COSMIC: COSV50192828;