16-51944704-C-A

Variant names:

• chr16-51944704-C-A
• rs8043960

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 0.673 in 152,060 control chromosomes in the GnomAD database, including 34,591 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 0.67 (34591 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 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: 0.673 AC: 102291 AN: 151942 Hom.: 34550 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.673 AC: 102399 AN: 152060 Hom.: 34591 Cov.: 32 AF XY: 0.672 AC XY: 49987 AN XY: 74334

African (AFR) AF: 0.646 AC: 26806 AN: 41470

American (AMR) AF: 0.714 AC: 10905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2566 AN: 3468

East Asian (EAS) AF: 0.774 AC: 4005 AN: 5172

South Asian (SAS) AF: 0.666 AC: 3203 AN: 4812

European-Finnish (FIN) AF: 0.628 AC: 6623 AN: 10540

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45918 AN: 67996

Other (OTH) AF: 0.697 AC: 1474 AN: 2114

Alfa AF: 0.682 Hom.: 58884

Bravo AF: 0.683

Asia WGS AF: 0.746 AC: 2596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.54
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs8043960; hg19: chr16-51978616;