rs11645366

chr16-62343249-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;