chr16-82609046-A-T

Variant names:

• chr16-82609046-A-T
• rs11646213

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 0.471 in 152,102 control chromosomes in the GnomAD database, including 19,003 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 0.47 (19003 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.597 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: 0.472 AC: 71683 AN: 151984 Hom.: 18994 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.471 AC: 71712 AN: 152102 Hom.: 19003 Cov.: 33 AF XY: 0.471 AC XY: 35047 AN XY: 74354

African (AFR) AF: 0.245 AC: 10166 AN: 41504

American (AMR) AF: 0.469 AC: 7156 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1951 AN: 3472

East Asian (EAS) AF: 0.181 AC: 937 AN: 5180

South Asian (SAS) AF: 0.510 AC: 2460 AN: 4822

European-Finnish (FIN) AF: 0.608 AC: 6420 AN: 10554

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40888 AN: 67980

Other (OTH) AF: 0.480 AC: 1013 AN: 2110

Alfa AF: 0.563 Hom.: 13935

Bravo AF: 0.447

Asia WGS AF: 0.327 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.47
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11646213; hg19: chr16-82642651;