rs1948632

Variant names:

• chr16-75957548-G-A
• rs1948632

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 0.733 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.733 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

Gnomad4 AFR AF: 0.891

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.653

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.713

Alfa AF: 0.665 Hom.: 55045

Bravo AF: 0.738

Asia WGS AF: 0.799 AC: 2776 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1948632; hg19: chr16-75991446;