chr16-48843720-A-G

Variant names:

• chr16-48843720-A-G
• rs1872694

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 0.637 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.637 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

African (AFR) AF: 0.692 AC: 28633 AN: 41376

American (AMR) AF: 0.720 AC: 11004 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.337 AC: 1736 AN: 5156

South Asian (SAS) AF: 0.701 AC: 3369 AN: 4808

European-Finnish (FIN) AF: 0.629 AC: 6623 AN: 10536

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41265 AN: 67956

Other (OTH) AF: 0.644 AC: 1358 AN: 2108

Alfa AF: 0.621 Hom.: 55715

Bravo AF: 0.643

Asia WGS AF: 0.598 AC: 2077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1872694; hg19: chr16-48877631;