rs17147986

Variant names:

• chr10-5996515-C-A
• rs17147986

Your query was ambiguous. Multiple possible variants found:

• chr10-5996515-C-A
• chr10-5996515-C-T

Variant summary

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

The variant allele was found at a frequency of 0.129 in 152,092 control chromosomes in the GnomAD database, including 1,355 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 0.13 (1355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.158 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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19597 AN: 151976 Hom.: 1357 Cov.: 32

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0771

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.129 AC: 19604 AN: 152092 Hom.: 1355 Cov.: 32 AF XY: 0.126 AC XY: 9376 AN XY: 74336

African (AFR) AF: 0.0943 AC: 3913 AN: 41490

American (AMR) AF: 0.0770 AC: 1177 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3472

East Asian (EAS) AF: 0.134 AC: 692 AN: 5174

South Asian (SAS) AF: 0.165 AC: 792 AN: 4806

European-Finnish (FIN) AF: 0.125 AC: 1324 AN: 10576

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10941 AN: 67984

Other (OTH) AF: 0.115 AC: 242 AN: 2110

Alfa AF: 0.140 Hom.: 1987

Bravo AF: 0.122

Asia WGS AF: 0.159 AC: 553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.19
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs17147986; hg19: chr10-6038478;