rs1478435

chr5-1454497-T-C

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 0.741 in 152,214 control chromosomes in the GnomAD database, including 41,924 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 0.74 (41924 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.807 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: 0.741 AC: 112633 AN: 152096 Hom.: 41891 Cov.: 34

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.741 AC: 112715 AN: 152214 Hom.: 41924 Cov.: 34 AF XY: 0.744 AC XY: 55368 AN XY: 74420

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.739

Alfa AF: 0.731 Hom.: 5061

Bravo AF: 0.739

Asia WGS AF: 0.732 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.25
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1478435; hg19: chr5-1454612;