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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374660	XR_001742606.2	n.502+71270C>T		intron_variant	Intron 3 of 3
LOC105374660	XR_007058696.1	n.766+11013C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;