16-28941317-T-C

Variant names:

• chr16-28941317-T-C
• rs11639897

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 0.762 in 150,572 control chromosomes in the GnomAD database, including 44,963 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 0.76 (44963 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 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: 0.762 AC: 114694 AN: 150458 Hom.: 44917 Cov.: 26

Gnomad AFR AF: 0.939

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.762 AC: 114786 AN: 150572 Hom.: 44963 Cov.: 26 AF XY: 0.762 AC XY: 55969 AN XY: 73456

African (AFR) AF: 0.939 AC: 38555 AN: 41046

American (AMR) AF: 0.645 AC: 9710 AN: 15064

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2664 AN: 3452

East Asian (EAS) AF: 0.905 AC: 4636 AN: 5120

South Asian (SAS) AF: 0.779 AC: 3734 AN: 4792

European-Finnish (FIN) AF: 0.690 AC: 7023 AN: 10172

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 45894 AN: 67638

Other (OTH) AF: 0.768 AC: 1600 AN: 2084

Alfa AF: 0.713 Hom.: 4911

Bravo AF: 0.767

Asia WGS AF: 0.799 AC: 2780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.085
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11639897; hg19: chr16-28952638;