chr11-115528028-A-T

Variant names:

• chr11-115528028-A-T
• rs7483296

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 0.129 in 152,092 control chromosomes in the GnomAD database, including 1,636 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 0.13 (1636 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 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: 0.129 AC: 19674 AN: 151974 Hom.: 1638 Cov.: 31

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.129 AC: 19671 AN: 152092 Hom.: 1636 Cov.: 31 AF XY: 0.129 AC XY: 9563 AN XY: 74328

African (AFR) AF: 0.0429 AC: 1782 AN: 41502

American (AMR) AF: 0.116 AC: 1777 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3466

East Asian (EAS) AF: 0.0505 AC: 261 AN: 5168

South Asian (SAS) AF: 0.300 AC: 1439 AN: 4802

European-Finnish (FIN) AF: 0.0851 AC: 901 AN: 10592

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12352 AN: 67968

Other (OTH) AF: 0.139 AC: 294 AN: 2110

Alfa AF: 0.145 Hom.: 225

Bravo AF: 0.122

Asia WGS AF: 0.143 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.8
DANN	Benign	0.90
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7483296; hg19: chr11-115398746;