rs11854147

Variant names:

• chr15-74760430-T-C
• rs11854147

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 0.529 in 151,990 control chromosomes in the GnomAD database, including 23,977 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 0.53 (23977 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.686 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: 0.530 AC: 80426 AN: 151872 Hom.: 23972 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.529 AC: 80444 AN: 151990 Hom.: 23977 Cov.: 31 AF XY: 0.524 AC XY: 38912 AN XY: 74280

African (AFR) AF: 0.275 AC: 11383 AN: 41432

American (AMR) AF: 0.434 AC: 6622 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2312 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1996 AN: 5166

South Asian (SAS) AF: 0.489 AC: 2356 AN: 4814

European-Finnish (FIN) AF: 0.658 AC: 6964 AN: 10576

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.691 AC: 46975 AN: 67964

Other (OTH) AF: 0.549 AC: 1160 AN: 2112

Alfa AF: 0.609 Hom.: 5908

Bravo AF: 0.503

Asia WGS AF: 0.470 AC: 1638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.27
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11854147; hg19: chr15-75052771;