rs11856413

Variant names:

• chr15-74907551-A-G
• rs11856413

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.353 in 152,122 control chromosomes in the GnomAD database, including 12,245 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 0.35 (12245 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 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: 0.353 AC: 53630 AN: 152004 Hom.: 12246 Cov.: 32

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.353 AC: 53635 AN: 152122 Hom.: 12245 Cov.: 32 AF XY: 0.341 AC XY: 25370 AN XY: 74378

Gnomad4 AFR AF: 0.0972

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.359

Alfa AF: 0.474 Hom.: 23505

Bravo AF: 0.349

Asia WGS AF: 0.121 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11856413; hg19: chr15-75199892;