16-75957548-G-A

Variant names:

• chr16-75957548-G-A
• rs1948632

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 0.733 in 152,046 control chromosomes in the GnomAD database, including 41,780 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 0.73 (41780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111307 AN: 151928 Hom.: 41734 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.733 AC: 111412 AN: 152046 Hom.: 41780 Cov.: 32 AF XY: 0.736 AC XY: 54734 AN XY: 74320

African (AFR) AF: 0.891 AC: 36993 AN: 41508

American (AMR) AF: 0.728 AC: 11114 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2265 AN: 3470

East Asian (EAS) AF: 0.794 AC: 4117 AN: 5182

South Asian (SAS) AF: 0.740 AC: 3570 AN: 4826

European-Finnish (FIN) AF: 0.689 AC: 7257 AN: 10538

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43796 AN: 67934

Other (OTH) AF: 0.713 AC: 1502 AN: 2106

Alfa AF: 0.676 Hom.: 140667

Bravo AF: 0.738

Asia WGS AF: 0.799 AC: 2776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.37
DANN	Benign	0.36
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs1948632; hg19: chr16-75991446;