16-31025699-A-T

Variant names:

• chr16-31025699-A-T
• rs11150604

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 0.323 in 152,034 control chromosomes in the GnomAD database, including 10,148 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 0.32 (10148 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 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: 0.323 AC: 49065 AN: 151916 Hom.: 10141 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.323 AC: 49090 AN: 152034 Hom.: 10148 Cov.: 31 AF XY: 0.326 AC XY: 24234 AN XY: 74310

African (AFR) AF: 0.108 AC: 4484 AN: 41520

American (AMR) AF: 0.393 AC: 5980 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4594 AN: 5152

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.393 AC: 4155 AN: 10574

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25818 AN: 67954

Other (OTH) AF: 0.390 AC: 823 AN: 2108

Alfa AF: 0.339 Hom.: 1423

Bravo AF: 0.327

Asia WGS AF: 0.472 AC: 1646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.72
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11150604; hg19: chr16-31037020;