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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.0770

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.115

Alfa AF: 0.143 Hom.: 1647

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17147986; hg19: chr10-6038478;