rs1318743

Positions:

• chr5-41587300-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504215.1(ENSG00000251478):​n.488A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0451 in 424,716 control chromosomes in the GnomAD database, including 1,764 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 0.038 (466 hom., cov: 33)
  • Exomes 𝑓: 0.049 (1298 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.74

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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
	ENST00000504215.1	n.488A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.0376 AC: 5724 AN: 152180 Hom.: 467 Cov.: 33

Gnomad AFR AF: 0.0388

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0431

GnomAD4 exome AF: 0.0493 AC: 13426 AN: 272418 Hom.: 1298 Cov.: 0 AF XY: 0.0550 AC XY: 8369 AN XY: 152142

Gnomad4 AFR exome AF: 0.0370

Gnomad4 AMR exome AF: 0.0122

Gnomad4 ASJ exome AF: 0.0196

Gnomad4 EAS exome AF: 0.365

Gnomad4 SAS exome AF: 0.124

Gnomad4 FIN exome AF: 0.00899

Gnomad4 NFE exome AF: 0.0139

Gnomad4 OTH exome AF: 0.0412

GnomAD4 genome AF: 0.0376 AC: 5719 AN: 152298 Hom.: 466 Cov.: 33 AF XY: 0.0405 AC XY: 3017 AN XY: 74466

Gnomad4 AFR AF: 0.0386

Gnomad4 AMR AF: 0.0212

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0237 Hom.: 118

Bravo AF: 0.0381

Asia WGS AF: 0.236 AC: 822 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	2.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1318743; hg19: chr5-41587402;