rs11072508

Variant names:

• chr15-74770056-C-T
• rs11072508

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 0.433 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
• Publications: 30 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.117 AC: 4850 AN: 41530

American (AMR) AF: 0.355 AC: 5433 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1943 AN: 3466

East Asian (EAS) AF: 0.175 AC: 904 AN: 5180

South Asian (SAS) AF: 0.197 AC: 949 AN: 4826

European-Finnish (FIN) AF: 0.556 AC: 5882 AN: 10572

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44368 AN: 67974

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.565 Hom.: 43333

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
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs11072508; hg19: chr15-75062397;