rs10517702

Variant names:

• chr4-159367288-T-C
• rs10517702
• ENST00000837042.1:n.549T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-159367288-T-C
• chr4-159367288-T-G

Variant summary

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

The ENST00000837042.1(ENSG00000308878):​n.549T>C 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 0.615 in 152,104 control chromosomes in the GnomAD database, including 30,082 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 0.62 (30082 hom., cov: 32)
• Consequence: ENSG00000308878 ENST00000837042.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 5 publications found

Genes affected

ENSG00000308878 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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
ENSG00000308878	ENST00000837042.1	n.549T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308878	ENST00000837043.1	n.614T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93488 AN: 151986 Hom.: 30045 Cov.: 32

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.615 AC: 93585 AN: 152104 Hom.: 30082 Cov.: 32 AF XY: 0.605 AC XY: 44988 AN XY: 74350

African (AFR) AF: 0.768 AC: 31859 AN: 41484

American (AMR) AF: 0.576 AC: 8798 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1661 AN: 3468

East Asian (EAS) AF: 0.110 AC: 570 AN: 5184

South Asian (SAS) AF: 0.430 AC: 2073 AN: 4826

European-Finnish (FIN) AF: 0.539 AC: 5685 AN: 10544

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 41034 AN: 67996

Other (OTH) AF: 0.574 AC: 1212 AN: 2110

Alfa AF: 0.572 Hom.: 3030

Bravo AF: 0.624

Asia WGS AF: 0.311 AC: 1082 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10517702; hg19: chr4-160288440;