rs9936750

Variant names:

• chr16-55137962-T-C
• rs9936750

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;