rs11639532

chr16-175160-G-Achr16-175160-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;