rs10517160

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0127 AC: 526 AN: 41506

American (AMR) AF: 0.0426 AC: 650 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4820

European-Finnish (FIN) AF: 0.0209 AC: 221 AN: 10566

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4841 AN: 67980

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0613 Hom.: 174

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
PhyloP100		0.0050

Splicing

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

Publications

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Other links and lift over

dbSNP: rs10517160; hg19: chr4-46509524;