rs9936750

Positions:

• chr16-55137962-T-C

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 0.15 in 152,188 control chromosomes in the GnomAD database, including 2,117 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 0.15 (2117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22805 AN: 152070 Hom.: 2118 Cov.: 32

Gnomad AFR AF: 0.0433

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.150 AC: 22796 AN: 152188 Hom.: 2117 Cov.: 32 AF XY: 0.150 AC XY: 11157 AN XY: 74382

Gnomad4 AFR AF: 0.0433

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.129

Alfa AF: 0.186 Hom.: 1671

Bravo AF: 0.137

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9936750; hg19: chr16-55171874;