16-52797550-T-C

Variant names:

• chr16-52797550-T-C
• rs6499100

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 0.43 in 151,860 control chromosomes in the GnomAD database, including 15,260 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 0.43 (15260 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 9 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 = 0.727 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: 0.430 AC: 65298 AN: 151742 Hom.: 15260 Cov.: 31

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.430 AC: 65322 AN: 151860 Hom.: 15260 Cov.: 31 AF XY: 0.434 AC XY: 32222 AN XY: 74198

African (AFR) AF: 0.260 AC: 10771 AN: 41460

American (AMR) AF: 0.582 AC: 8876 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3856 AN: 5164

South Asian (SAS) AF: 0.451 AC: 2164 AN: 4802

European-Finnish (FIN) AF: 0.522 AC: 5488 AN: 10518

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31094 AN: 67888

Other (OTH) AF: 0.459 AC: 965 AN: 2102

Alfa AF: 0.456 Hom.: 53656

Bravo AF: 0.438

Asia WGS AF: 0.535 AC: 1859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.58
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs6499100; hg19: chr16-52831462; COSMIC: COSV56529876;