rs11639532

Variant names:

• chr16-175160-G-A
• rs11639532

Your query was ambiguous. Multiple possible variants found:

• chr16-175160-G-A
• chr16-175160-G-C

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 0.188 in 147,790 control chromosomes in the GnomAD database, including 3,797 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 0.19 (3797 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.248 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: 0.188 AC: 27769 AN: 147672 Hom.: 3792 Cov.: 30

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.188 AC: 27793 AN: 147790 Hom.: 3797 Cov.: 30 AF XY: 0.188 AC XY: 13582 AN XY: 72150

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.190

Alfa AF: 0.169 Hom.: 1293

Bravo AF: 0.195

Asia WGS AF: 0.248 AC: 814 AN: 3284

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.55
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11639532; hg19: chr16-225159;