chr11-12590302-T-G

Variant names:

• chr11-12590302-T-G
• rs10765970

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 0.192 in 152,090 control chromosomes in the GnomAD database, including 3,574 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 0.19 (3574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.588 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: 0.192 AC: 29128 AN: 151970 Hom.: 3578 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.0820

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.192 AC: 29145 AN: 152090 Hom.: 3574 Cov.: 32 AF XY: 0.201 AC XY: 14945 AN XY: 74348

African (AFR) AF: 0.230 AC: 9529 AN: 41476

American (AMR) AF: 0.236 AC: 3611 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0820 AC: 284 AN: 3464

East Asian (EAS) AF: 0.606 AC: 3134 AN: 5170

South Asian (SAS) AF: 0.328 AC: 1576 AN: 4804

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8798 AN: 68004

Other (OTH) AF: 0.145 AC: 306 AN: 2110

Alfa AF: 0.145 Hom.: 3674

Bravo AF: 0.197

Asia WGS AF: 0.434 AC: 1507 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	0.55
DANN	Benign	0.36
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs10765970; hg19: chr11-12611849;