rs11072508

Positions:

• chr15-74770056-C-T

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 0.433 in 152,166 control chromosomes in the GnomAD database, including 18,641 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 0.43 (18641 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74770056C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65883 AN: 152048 Hom.: 18647 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.433 AC: 65861 AN: 152166 Hom.: 18641 Cov.: 33 AF XY: 0.420 AC XY: 31225 AN XY: 74392

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.453

Alfa AF: 0.555 Hom.: 4519

Bravo AF: 0.412

Asia WGS AF: 0.169 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11072508; hg19: chr15-75062397;