rs10517313

Variant names:

• chr4-53844785-G-A
• rs10517313
• ENST00000507166.5:c.1017+418820G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-53844785-G-A
• chr4-53844785-G-C
• chr4-53844785-G-T

Variant summary

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

The ENST00000507166.5(ENSG00000282278):​c.1017+418820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,942 control chromosomes in the GnomAD database, including 26,762 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 0.56 (26762 hom., cov: 31)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 4 publications found

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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
ENSG00000282278	ENST00000507166.5	c.1017+418820G>A		intron_variant	Intron 12 of 23	2		ENSP00000423325.1

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85413 AN: 151824 Hom.: 26760 Cov.: 31

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.539

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.562 AC: 85442 AN: 151942 Hom.: 26762 Cov.: 31 AF XY: 0.578 AC XY: 42951 AN XY: 74252

African (AFR) AF: 0.270 AC: 11203 AN: 41420

American (AMR) AF: 0.678 AC: 10348 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2409 AN: 3470

East Asian (EAS) AF: 0.870 AC: 4502 AN: 5176

South Asian (SAS) AF: 0.847 AC: 4078 AN: 4816

European-Finnish (FIN) AF: 0.754 AC: 7957 AN: 10560

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43004 AN: 67928

Other (OTH) AF: 0.592 AC: 1247 AN: 2106

Alfa AF: 0.621 Hom.: 19259

Bravo AF: 0.542

Asia WGS AF: 0.796 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.39
PhyloP100		0.0030
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10517313; hg19: chr4-54710952;