rs3756008

Positions:

• chr4-186264231-A-T

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 0.359 in 152,054 control chromosomes in the GnomAD database, including 10,081 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 0.36 (10081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 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: 0.359 AC: 54531 AN: 151936 Hom.: 10063 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.359 AC: 54580 AN: 152054 Hom.: 10081 Cov.: 32 AF XY: 0.358 AC XY: 26598 AN XY: 74292

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.391

Alfa AF: 0.392 Hom.: 6815

Bravo AF: 0.350

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3756008; hg19: chr4-187185385;