rs1348478

Positions:

• chr5-120098498-G-A
• chr5-120098498-G-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 0.307 in 151,536 control chromosomes in the GnomAD database, including 11,690 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 0.31 (11690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.306 AC: 46381 AN: 151418 Hom.: 11653 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.307 AC: 46469 AN: 151536 Hom.: 11690 Cov.: 32 AF XY: 0.306 AC XY: 22666 AN XY: 74052

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.266

Alfa AF: 0.155 Hom.: 5096

Bravo AF: 0.326

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1348478; hg19: chr5-119434193;