rs10517160

Variant names:

• chr4-46507507-G-A
• rs10517160
• ENST00000651612.1:n.618G>A

Variant summary

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

The ENST00000651612.1(ENSG00000249330):​n.618G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0451 in 152,096 control chromosomes in the GnomAD database, including 229 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 0.045 (229 hom., cov: 32)
• Consequence: ENSG00000249330 ENST00000651612.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

Genes affected

ENSG00000249330 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0695 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
ENSG00000249330	ENST00000651612.1	n.618G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0451 AC: 6857 AN: 151978 Hom.: 229 Cov.: 32

Gnomad AFR AF: 0.0127

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0187

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0531

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

GnomAD4 genome AF: 0.0451 AC: 6853 AN: 152096 Hom.: 229 Cov.: 32 AF XY: 0.0423 AC XY: 3148 AN XY: 74366

Gnomad4 AFR AF: 0.0127

Gnomad4 AMR AF: 0.0426

Gnomad4 ASJ AF: 0.0692

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.0209

Gnomad4 NFE AF: 0.0712

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0601 Hom.: 158

Bravo AF: 0.0464

Asia WGS AF: 0.00779 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.3
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517160; hg19: chr4-46509524;