16-62651092-G-T

Variant names:

• chr16-62651092-G-T
• rs1027277

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 0.404 in 152,066 control chromosomes in the GnomAD database, including 12,998 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 0.40 (12998 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.404 AC: 61350 AN: 151948 Hom.: 12995 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.404 AC: 61376 AN: 152066 Hom.: 12998 Cov.: 32 AF XY: 0.402 AC XY: 29897 AN XY: 74302

African (AFR) AF: 0.272 AC: 11294 AN: 41486

American (AMR) AF: 0.398 AC: 6082 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1302 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2517 AN: 5170

South Asian (SAS) AF: 0.371 AC: 1785 AN: 4810

European-Finnish (FIN) AF: 0.481 AC: 5082 AN: 10568

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31921 AN: 67964

Other (OTH) AF: 0.388 AC: 820 AN: 2116

Alfa AF: 0.442 Hom.: 51024

Bravo AF: 0.393

Asia WGS AF: 0.389 AC: 1351 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.37
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1027277; hg19: chr16-62684996; COSMIC: COSV66151087;