rs494270

Variant names:

• chr4-46194058-T-A
• rs494270

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 0.481 in 151,698 control chromosomes in the GnomAD database, including 19,223 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 0.48 (19223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.748 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: 0.481 AC: 72908 AN: 151580 Hom.: 19222 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.481 AC: 72922 AN: 151698 Hom.: 19223 Cov.: 32 AF XY: 0.486 AC XY: 36033 AN XY: 74114

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.523

Alfa AF: 0.500 Hom.: 2498

Bravo AF: 0.459

Asia WGS AF: 0.608 AC: 2096 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs494270; hg19: chr4-46196075;