rs1494673

Variant names:

• chr5-124538305-C-T
• rs1494673

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 0.124 in 152,170 control chromosomes in the GnomAD database, including 1,397 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 0.12 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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: 0.124 AC: 18866 AN: 152052 Hom.: 1398 Cov.: 32

Gnomad AFR AF: 0.0399

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.124 AC: 18858 AN: 152170 Hom.: 1397 Cov.: 32 AF XY: 0.123 AC XY: 9164 AN XY: 74392

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.129

Alfa AF: 0.163 Hom.: 4269

Bravo AF: 0.116

Asia WGS AF: 0.106 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494673; hg19: chr5-123873998;