16-81230992-T-G

Variant names:

• chr16-81230992-T-G
• rs6564851

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 0.489 in 152,072 control chromosomes in the GnomAD database, including 18,836 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 0.49 (18836 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 76 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74293 AN: 151954 Hom.: 18830 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.489 AC: 74330 AN: 152072 Hom.: 18836 Cov.: 33 AF XY: 0.495 AC XY: 36778 AN XY: 74322

African (AFR) AF: 0.386 AC: 16012 AN: 41460

American (AMR) AF: 0.512 AC: 7826 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1478 AN: 3468

East Asian (EAS) AF: 0.815 AC: 4221 AN: 5178

South Asian (SAS) AF: 0.511 AC: 2458 AN: 4814

European-Finnish (FIN) AF: 0.601 AC: 6351 AN: 10570

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34423 AN: 67988

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.501 Hom.: 93959

Bravo AF: 0.482

Asia WGS AF: 0.667 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs6564851; hg19: chr16-81264597;