rs11812365

Variant names:

• chr10-49261236-T-C
• rs11812365

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 0.176 in 148,652 control chromosomes in the GnomAD database, including 2,651 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 0.18 (2651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 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: 0.176 AC: 26190 AN: 148544 Hom.: 2648 Cov.: 31

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.176 AC: 26204 AN: 148652 Hom.: 2651 Cov.: 31 AF XY: 0.177 AC XY: 12798 AN XY: 72220

African (AFR) AF: 0.284 AC: 11514 AN: 40566

American (AMR) AF: 0.140 AC: 2069 AN: 14728

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 511 AN: 3440

East Asian (EAS) AF: 0.105 AC: 521 AN: 4944

South Asian (SAS) AF: 0.185 AC: 848 AN: 4588

European-Finnish (FIN) AF: 0.194 AC: 1931 AN: 9936

Middle Eastern (MID) AF: 0.0979 AC: 28 AN: 286

European-Non Finnish (NFE) AF: 0.123 AC: 8291 AN: 67242

Other (OTH) AF: 0.170 AC: 345 AN: 2026

Alfa AF: 0.143 Hom.: 1681

Bravo AF: 0.174

Asia WGS AF: 0.159 AC: 551 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.75
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs11812365; hg19: chr10-50469281;