rs3756009

Variant names:

• chr4-186264957-A-G
• rs3756009

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 0.32 in 152,046 control chromosomes in the GnomAD database, including 8,654 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 0.32 (8654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 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: 0.320 AC: 48610 AN: 151928 Hom.: 8643 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.320 AC: 48634 AN: 152046 Hom.: 8654 Cov.: 32 AF XY: 0.320 AC XY: 23754 AN XY: 74314

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.359

Alfa AF: 0.374 Hom.: 10842

Bravo AF: 0.309

Asia WGS AF: 0.327 AC: 1138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.74
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756009; hg19: chr4-187186111;