rs11760836

Variant names:

• chr7-15090328-T-G
• rs11760836

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 0.0215 in 152,266 control chromosomes in the GnomAD database, including 70 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 0.021 (70 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.072 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: 0.0214 AC: 3254 AN: 152148 Hom.: 70 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0592

Gnomad ASJ AF: 0.00865

Gnomad EAS AF: 0.0777

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0215 AC: 3271 AN: 152266 Hom.: 70 Cov.: 32 AF XY: 0.0236 AC XY: 1755 AN XY: 74450

African (AFR) AF: 0.0135 AC: 561 AN: 41546

American (AMR) AF: 0.0597 AC: 913 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00865 AC: 30 AN: 3470

East Asian (EAS) AF: 0.0783 AC: 406 AN: 5188

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4830

European-Finnish (FIN) AF: 0.0303 AC: 321 AN: 10602

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0140 AC: 953 AN: 68016

Other (OTH) AF: 0.0118 AC: 25 AN: 2114

Alfa AF: 0.0177 Hom.: 59

Bravo AF: 0.0237

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs11760836; hg19: chr7-15129953;