chr11-15812277-A-T

Variant names:

• chr11-15812277-A-T
• rs1440714

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 0.406 in 151,752 control chromosomes in the GnomAD database, including 14,504 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 0.41 (14504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.599
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 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: 0.406 AC: 61544 AN: 151634 Hom.: 14461 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.406 AC: 61644 AN: 151752 Hom.: 14504 Cov.: 32 AF XY: 0.405 AC XY: 30041 AN XY: 74146

African (AFR) AF: 0.634 AC: 26265 AN: 41438

American (AMR) AF: 0.489 AC: 7437 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3466

East Asian (EAS) AF: 0.238 AC: 1225 AN: 5156

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4814

European-Finnish (FIN) AF: 0.250 AC: 2633 AN: 10540

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19975 AN: 67836

Other (OTH) AF: 0.372 AC: 782 AN: 2104

Alfa AF: 0.367 Hom.: 1412

Bravo AF: 0.434

Asia WGS AF: 0.386 AC: 1328 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.7
DANN	Benign	0.67
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1440714; hg19: chr11-15833823;