rs11072507

Variant names:

• chr15-74762525-G-C
• rs11072507

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.431 in 152,028 control chromosomes in the GnomAD database, including 18,459 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 (18459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.644 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: 0.431 AC: 65532 AN: 151910 Hom.: 18465 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.431 AC: 65513 AN: 152028 Hom.: 18459 Cov.: 32 AF XY: 0.418 AC XY: 31077 AN XY: 74308

African (AFR) AF: 0.115 AC: 4775 AN: 41454

American (AMR) AF: 0.353 AC: 5397 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3470

East Asian (EAS) AF: 0.179 AC: 920 AN: 5148

South Asian (SAS) AF: 0.193 AC: 932 AN: 4820

European-Finnish (FIN) AF: 0.560 AC: 5920 AN: 10580

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44142 AN: 67962

Other (OTH) AF: 0.449 AC: 949 AN: 2114

Alfa AF: 0.530 Hom.: 3054

Bravo AF: 0.410

Asia WGS AF: 0.175 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs11072507; hg19: chr15-75054866; COSMIC: COSV53304699;