16-13813331-A-G

Variant names:

• chr16-13813331-A-G
• rs743672

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 0.118 in 152,170 control chromosomes in the GnomAD database, including 1,390 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 0.12 (1390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.549
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 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: 0.118 AC: 17940 AN: 152052 Hom.: 1388 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.118 AC: 17974 AN: 152170 Hom.: 1390 Cov.: 32 AF XY: 0.119 AC XY: 8880 AN XY: 74424

African (AFR) AF: 0.213 AC: 8825 AN: 41482

American (AMR) AF: 0.110 AC: 1689 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3472

East Asian (EAS) AF: 0.121 AC: 623 AN: 5166

South Asian (SAS) AF: 0.109 AC: 527 AN: 4814

European-Finnish (FIN) AF: 0.0704 AC: 748 AN: 10622

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4678 AN: 68008

Other (OTH) AF: 0.112 AC: 236 AN: 2116

Alfa AF: 0.0836 Hom.: 1093

Bravo AF: 0.128

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.7
DANN	Benign	0.53
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs743672; hg19: chr16-13907188;