16-175160-G-A

Variant names:

• chr16-175160-G-A
• rs11639532

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 0.188 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
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• 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

African (AFR) AF: 0.235 AC: 8910 AN: 37950

American (AMR) AF: 0.204 AC: 3072 AN: 15086

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3462

East Asian (EAS) AF: 0.178 AC: 914 AN: 5126

South Asian (SAS) AF: 0.260 AC: 1211 AN: 4652

European-Finnish (FIN) AF: 0.143 AC: 1488 AN: 10440

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.161 AC: 10931 AN: 67800

Other (OTH) AF: 0.190 AC: 396 AN: 2080

Alfa AF: 0.168 Hom.: 1712

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11639532; hg19: chr16-225159;