16-31249101-A-G

Variant names:

• chr16-31249101-A-G
• rs889551

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 0.73 in 151,946 control chromosomes in the GnomAD database, including 41,382 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 (41382 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 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: 0.730 AC: 110799 AN: 151828 Hom.: 41347 Cov.: 30

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.730 AC: 110887 AN: 151946 Hom.: 41382 Cov.: 30 AF XY: 0.722 AC XY: 53602 AN XY: 74270

African (AFR) AF: 0.890 AC: 36906 AN: 41460

American (AMR) AF: 0.661 AC: 10064 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3753 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2163 AN: 4810

European-Finnish (FIN) AF: 0.623 AC: 6584 AN: 10560

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46250 AN: 67940

Other (OTH) AF: 0.746 AC: 1571 AN: 2106

Alfa AF: 0.696 Hom.: 4109

Bravo AF: 0.747

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.7
DANN	Benign	0.66
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs889551; hg19: chr16-31260422;