4-35902002-C-T

Variant names:

• chr4-35902002-C-T
• rs753920

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 0.137 in 152,142 control chromosomes in the GnomAD database, including 1,746 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 0.14 (1746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.174 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: 0.137 AC: 20780 AN: 152024 Hom.: 1742 Cov.: 32

Gnomad AFR AF: 0.0709

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0580

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.137 AC: 20791 AN: 152142 Hom.: 1746 Cov.: 32 AF XY: 0.135 AC XY: 10047 AN XY: 74352

Gnomad4 AFR AF: 0.0708

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0576

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.159

Alfa AF: 0.175 Hom.: 5261

Bravo AF: 0.129

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753920; hg19: chr4-35903624;