chr16-62343249-C-T

Variant names:

• chr16-62343249-C-T
• rs11645366

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.167 in 152,014 control chromosomes in the GnomAD database, including 2,685 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 0.17 (2685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.167 AC: 25329 AN: 151896 Hom.: 2687 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.167 AC: 25324 AN: 152014 Hom.: 2685 Cov.: 32 AF XY: 0.168 AC XY: 12451 AN XY: 74296

Gnomad4 AFR AF: 0.0466

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.186

Alfa AF: 0.215 Hom.: 7583

Bravo AF: 0.155

Asia WGS AF: 0.184 AC: 642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11645366; hg19: chr16-62377153;