11-37849431-T-C

Variant names:

• chr11-37849431-T-C
• rs16930685

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 0.166 in 152,044 control chromosomes in the GnomAD database, including 2,891 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 (2891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25175 AN: 151924 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.166 AC: 25209 AN: 152044 Hom.: 2891 Cov.: 32 AF XY: 0.168 AC XY: 12466 AN XY: 74334

African (AFR) AF: 0.328 AC: 13622 AN: 41474

American (AMR) AF: 0.160 AC: 2443 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.0655 AC: 227 AN: 3468

East Asian (EAS) AF: 0.166 AC: 859 AN: 5162

South Asian (SAS) AF: 0.200 AC: 962 AN: 4822

European-Finnish (FIN) AF: 0.0744 AC: 788 AN: 10590

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5933 AN: 67972

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.132 Hom.: 2233

Bravo AF: 0.178

Asia WGS AF: 0.208 AC: 724 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.59
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs16930685; hg19: chr11-37870981;