4-4877046-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 0.598 in 151,906 control chromosomes in the GnomAD database, including 27,707 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 0.60 (27707 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

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 (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.598 AC: 90796 AN: 151788 Hom.: 27656 Cov.: 31

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.804

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.598 AC: 90904 AN: 151906 Hom.: 27707 Cov.: 31 AF XY: 0.608 AC XY: 45116 AN XY: 74250

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.573

Alfa AF: 0.562 Hom.: 4932

Bravo AF: 0.588

Asia WGS AF: 0.711 AC: 2474 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	1.1
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4689955; hg19: chr4-4878773;