rs3846271

Variant names:

• chr4-170155242-T-A
• rs3846271

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 0.031 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00599 AC: 249 AN: 41566

American (AMR) AF: 0.0502 AC: 768 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1539 AN: 5150

South Asian (SAS) AF: 0.137 AC: 663 AN: 4824

European-Finnish (FIN) AF: 0.0146 AC: 155 AN: 10624

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0180 AC: 1223 AN: 68030

Other (OTH) AF: 0.0251 AC: 53 AN: 2112

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
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs3846271; hg19: chr4-171076393;