4-3764538-T-C

Position:

• chr4-3764538-T-C

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 0.896 in 152,292 control chromosomes in the GnomAD database, including 61,617 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 0.90 (61617 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.97 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: 0.896 AC: 136330 AN: 152174 Hom.: 61553 Cov.: 35

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.896 AC: 136454 AN: 152292 Hom.: 61617 Cov.: 35 AF XY: 0.891 AC XY: 66312 AN XY: 74450

Gnomad4 AFR AF: 0.978

Gnomad4 AMR AF: 0.806

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.897

Gnomad4 OTH AF: 0.900

Alfa AF: 0.902 Hom.: 7699

Bravo AF: 0.894

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.070
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6846820; hg19: chr4-3766265;