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. Variant got -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

Genes affected

ENSG00000282278 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.847

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.592

Alfa AF: 0.625 Hom.: 17758

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517313; hg19: chr4-54710952;