rs9936750

Variant names:

• chr16-55137962-T-C
• rs9936750

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 0.15 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0433 AC: 1799 AN: 41572

American (AMR) AF: 0.118 AC: 1804 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0531 AC: 184 AN: 3466

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5162

South Asian (SAS) AF: 0.135 AC: 652 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2226 AN: 10580

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14671 AN: 67982

Other (OTH) AF: 0.129 AC: 272 AN: 2114

Alfa AF: 0.187 Hom.: 6298

Bravo AF: 0.137

Asia WGS AF: 0.152 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.84
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs9936750; hg19: chr16-55171874;