16-35853760-T-C

Variant names:

• chr16-35853760-T-C
• rs12599426

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 0.118 in 152,146 control chromosomes in the GnomAD database, including 1,510 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 0.12 (1510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18005 AN: 152026 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.0894

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.118 AC: 18017 AN: 152146 Hom.: 1510 Cov.: 32 AF XY: 0.125 AC XY: 9262 AN XY: 74372

African (AFR) AF: 0.0895 AC: 3717 AN: 41526

American (AMR) AF: 0.0893 AC: 1365 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1685 AN: 5148

South Asian (SAS) AF: 0.465 AC: 2240 AN: 4822

European-Finnish (FIN) AF: 0.109 AC: 1153 AN: 10594

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7076 AN: 67998

Other (OTH) AF: 0.123 AC: 259 AN: 2102

Alfa AF: 0.111 Hom.: 1311

Bravo AF: 0.108

Asia WGS AF: 0.398 AC: 1379 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.34
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs12599426; hg19: chr16-35088131;