16-82611001-C-T

Variant names:

• chr16-82611001-C-T
• rs7200895

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 0.787 in 152,130 control chromosomes in the GnomAD database, including 47,688 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 0.79 (47688 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 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: 0.787 AC: 119635 AN: 152012 Hom.: 47648 Cov.: 32

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.787 AC: 119732 AN: 152130 Hom.: 47688 Cov.: 32 AF XY: 0.780 AC XY: 57987 AN XY: 74370

African (AFR) AF: 0.762 AC: 31616 AN: 41470

American (AMR) AF: 0.728 AC: 11135 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2675 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2182 AN: 5174

South Asian (SAS) AF: 0.748 AC: 3604 AN: 4818

European-Finnish (FIN) AF: 0.797 AC: 8438 AN: 10584

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57397 AN: 68004

Other (OTH) AF: 0.769 AC: 1624 AN: 2112

Alfa AF: 0.814 Hom.: 6193

Bravo AF: 0.779

Asia WGS AF: 0.589 AC: 2052 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.2
DANN	Benign	0.45
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7200895; hg19: chr16-82644606;