4-54375414-C-T

Position:

• chr4-54375414-C-T

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 0.386 in 152,040 control chromosomes in the GnomAD database, including 11,705 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 0.39 (11705 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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 = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58646 AN: 151922 Hom.: 11686 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.386 AC: 58707 AN: 152040 Hom.: 11705 Cov.: 32 AF XY: 0.380 AC XY: 28228 AN XY: 74306

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.399

Alfa AF: 0.389 Hom.: 1537

Bravo AF: 0.395

Asia WGS AF: 0.234 AC: 815 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	0.27
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312648; hg19: chr4-55241581;