16-31249101-A-G

Variant names:

• chr16-31249101-A-G
• rs889551

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 0.73 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.890

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.746

Alfa AF: 0.685 Hom.: 3787

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs889551; hg19: chr16-31260422;