16-23012775-T-C

Variant names:

• chr16-23012775-T-C
• rs6497620

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 0.698 in 151,930 control chromosomes in the GnomAD database, including 37,952 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 0.70 (37952 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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: 0.698 AC: 105933 AN: 151812 Hom.: 37935 Cov.: 30

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.698 AC: 105995 AN: 151930 Hom.: 37952 Cov.: 30 AF XY: 0.696 AC XY: 51654 AN XY: 74246

African (AFR) AF: 0.835 AC: 34601 AN: 41426

American (AMR) AF: 0.515 AC: 7850 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2445 AN: 5142

South Asian (SAS) AF: 0.727 AC: 3502 AN: 4816

European-Finnish (FIN) AF: 0.697 AC: 7366 AN: 10572

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45360 AN: 67938

Other (OTH) AF: 0.687 AC: 1446 AN: 2106

Alfa AF: 0.679 Hom.: 95437

Bravo AF: 0.684

Asia WGS AF: 0.589 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6497620; hg19: chr16-23024096;