rs4463179

chr5-13505322-G-Achr5-13505322-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742606.2(LOC105374660):n.502+71270C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449

Genes affected

LOC105374660 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374660	XR_001742606.2	n.502+71270C>T		intron_variant, non_coding_transcript_variant
LOC105374660	XR_007058696.1	n.766+11013C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0840

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.0975

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.152

Alfa AF: 0.111 Hom.: 1249

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

Splicing

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

Publications

LitVar

Other links and lift over

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