4-53868344-T-C

Position:

• chr4-53868344-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 0.843 in 151,926 control chromosomes in the GnomAD database, including 55,115 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 0.84 (55115 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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: 0.843 AC: 127980 AN: 151810 Hom.: 55082 Cov.: 29

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.916

Gnomad ASJ AF: 0.888

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.843 AC: 128061 AN: 151926 Hom.: 55115 Cov.: 29 AF XY: 0.848 AC XY: 62946 AN XY: 74262

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.916

Gnomad4 ASJ AF: 0.888

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.862

Alfa AF: 0.901 Hom.: 86770

Bravo AF: 0.831

Asia WGS AF: 0.928 AC: 3226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1391758; hg19: chr4-54734511;