rs1872694

Positions:

• chr16-48843720-A-G

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 0.637 in 151,886 control chromosomes in the GnomAD database, including 31,253 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 0.64 (31253 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96690 AN: 151768 Hom.: 31209 Cov.: 31

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.635

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.637 AC: 96788 AN: 151886 Hom.: 31253 Cov.: 31 AF XY: 0.640 AC XY: 47474 AN XY: 74234

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.644

Alfa AF: 0.619 Hom.: 39909

Bravo AF: 0.643

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872694; hg19: chr16-48877631;