rs4886410

Variant names:

• chr15-74773303-G-C
• rs4886410

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 0.434 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
• Publications: 17 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 = 0.652 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: 0.435 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

African (AFR) AF: 0.117 AC: 4842 AN: 41486

American (AMR) AF: 0.358 AC: 5463 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1946 AN: 3472

East Asian (EAS) AF: 0.174 AC: 900 AN: 5160

South Asian (SAS) AF: 0.199 AC: 956 AN: 4814

European-Finnish (FIN) AF: 0.551 AC: 5800 AN: 10532

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44587 AN: 67890

Other (OTH) AF: 0.449 AC: 946 AN: 2106

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
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4886410; hg19: chr15-75065644;