rs3846271

chr4-170155242-T-A

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 0.031 in 152,276 control chromosomes in the GnomAD database, including 328 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 0.031 (328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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 (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0310 AC: 4719 AN: 152158 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.00601

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0499

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0310 AC: 4726 AN: 152276 Hom.: 328 Cov.: 32 AF XY: 0.0345 AC XY: 2567 AN XY: 74476

Gnomad4 AFR AF: 0.00599

Gnomad4 AMR AF: 0.0502

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0146

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0221 Hom.: 13

Bravo AF: 0.0339

Asia WGS AF: 0.193 AC: 671 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	5.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3846271; hg19: chr4-171076393;