rs10515108

Variant names:

• chr17-55689895-A-G
• rs10515108
• ENST00000847279.1:n.245-988A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-55689895-A-G
• chr17-55689895-A-T

Variant summary

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

The ENST00000847279.1(ENSG00000289016):​n.245-988A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,210 control chromosomes in the GnomAD database, including 1,807 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 0.14 (1807 hom., cov: 33)
• Consequence: ENSG00000289016 ENST00000847279.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 1 publications found

Genes affected

ENSG00000289016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904099	XR_007065976.1	n.56-988A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289016	ENST00000847279.1	n.245-988A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 21026 AN: 152092 Hom.: 1806 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0387

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.0951

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.138 AC: 21052 AN: 152210 Hom.: 1807 Cov.: 33 AF XY: 0.134 AC XY: 9992 AN XY: 74422

African (AFR) AF: 0.228 AC: 9459 AN: 41492

American (AMR) AF: 0.154 AC: 2352 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.117 AC: 607 AN: 5178

South Asian (SAS) AF: 0.125 AC: 602 AN: 4828

European-Finnish (FIN) AF: 0.0387 AC: 411 AN: 10622

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0951 AC: 6469 AN: 68016

Other (OTH) AF: 0.172 AC: 363 AN: 2116

Alfa AF: 0.125 Hom.: 417

Bravo AF: 0.151

Asia WGS AF: 0.142 AC: 492 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.3
DANN	Benign	0.31
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10515108; hg19: chr17-53767256;