4-54375414-C-T

Variant names:

• chr4-54375414-C-T
• rs9312648

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;