4-99446634-C-T

Position:

• chr4-99446634-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 0.318 in 151,776 control chromosomes in the GnomAD database, including 8,546 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 0.32 (8546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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 (AMR) allele frequency at 95% confidence interval = 0.387 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: 0.318 AC: 48291 AN: 151656 Hom.: 8543 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.318 AC: 48314 AN: 151776 Hom.: 8546 Cov.: 32 AF XY: 0.321 AC XY: 23809 AN XY: 74162

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.315

Alfa AF: 0.199 Hom.: 450

Bravo AF: 0.316

Asia WGS AF: 0.323 AC: 1126 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	3.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs749407; hg19: chr4-100367791;