rs1478435

Variant names:

• chr5-1454497-T-C
• rs1478435

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.787 AC: 32680 AN: 41524

American (AMR) AF: 0.750 AC: 11478 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2480 AN: 3470

East Asian (EAS) AF: 0.617 AC: 3193 AN: 5176

South Asian (SAS) AF: 0.829 AC: 4001 AN: 4828

European-Finnish (FIN) AF: 0.720 AC: 7631 AN: 10596

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48852 AN: 68002

Other (OTH) AF: 0.739 AC: 1563 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.25
DANN	Benign	0.14
PhyloP100		-3.7

Splicing

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

Other links and lift over

dbSNP: rs1478435; hg19: chr5-1454612;