rs4886410

Positions:

• chr15-74773303-G-C

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 0.434 in 151,944 control chromosomes in the GnomAD database, including 18,739 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 (18739 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

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 = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66039 AN: 151826 Hom.: 18746 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.434 AC: 66016 AN: 151944 Hom.: 18739 Cov.: 31 AF XY: 0.421 AC XY: 31268 AN XY: 74248

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.449

Alfa AF: 0.533 Hom.: 3072

Bravo AF: 0.414

Asia WGS AF: 0.166 AC: 583 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	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886410; hg19: chr15-75065644;