rs11072508

Variant names:

• chr15-74770056-C-T
• rs11072508

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;