4-46131526-C-T

Position:

• chr4-46131526-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 0.416 in 151,818 control chromosomes in the GnomAD database, including 13,767 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 0.42 (13767 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.491

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.416 AC: 63111 AN: 151700 Hom.: 13762 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.416 AC: 63141 AN: 151818 Hom.: 13767 Cov.: 32 AF XY: 0.412 AC XY: 30552 AN XY: 74160

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.412

Alfa AF: 0.436 Hom.: 1881

Bravo AF: 0.408

Asia WGS AF: 0.292 AC: 1015 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	11
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17639557; hg19: chr4-46133543;