rs13178964

Variant names:

• chr5-105011948-A-G
• rs13178964
• ENST00000503650.1:n.211-124973T>C

Variant summary

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

The ENST00000503650.1(ENSG00000251574):​n.211-124973T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 151,696 control chromosomes in the GnomAD database, including 2,409 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 (2409 hom., cov: 32)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000251574	ENST00000503650.1	n.211-124973T>C		intron_variant	Intron 1 of 2	3
ENSG00000253584	ENST00000522464.1	n.69-3037T>C		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25153 AN: 151578 Hom.: 2409 Cov.: 32

Gnomad AFR AF: 0.0830

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.166 AC: 25156 AN: 151696 Hom.: 2409 Cov.: 32 AF XY: 0.163 AC XY: 12050 AN XY: 74098

Gnomad4 AFR AF: 0.0831

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.205

Alfa AF: 0.197 Hom.: 511

Bravo AF: 0.160

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13178964; hg19: chr5-104347649; COSMIC: COSV72236289;