rs11760836

Positions:

• chr7-15090328-T-G

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.15090328T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0135

Gnomad4 AMR AF: 0.0597

Gnomad4 ASJ AF: 0.00865

Gnomad4 EAS AF: 0.0783

Gnomad4 SAS AF: 0.0108

Gnomad4 FIN AF: 0.0303

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0168 Hom.: 37

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11760836; hg19: chr7-15129953;