4-35901877-C-T

Variant names:

• chr4-35901877-C-T
• rs753921

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 0.272 in 152,040 control chromosomes in the GnomAD database, including 5,726 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 0.27 (5726 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

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 (SAS) allele frequency at 95% confidence interval = 0.302 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: 0.272 AC: 41322 AN: 151924 Hom.: 5724 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.272 AC: 41361 AN: 152040 Hom.: 5726 Cov.: 32 AF XY: 0.270 AC XY: 20067 AN XY: 74306

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.294

Alfa AF: 0.293 Hom.: 14080

Bravo AF: 0.271

Asia WGS AF: 0.255 AC: 886 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	3.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753921; hg19: chr4-35903499;