5-41586303-T-C

Position:

• chr5-41586303-T-C

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.1141A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 506,432 control chromosomes in the GnomAD database, including 40,421 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 0.41 (13419 hom., cov: 32)
  • Exomes 𝑓: 0.38 (27002 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.04

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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
	ENST00000504215.1	n.1141A>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62089 AN: 151862 Hom.: 13415 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.426

GnomAD4 exome AF: 0.380 AC: 134816 AN: 354452 Hom.: 27002 Cov.: 0 AF XY: 0.389 AC XY: 73460 AN XY: 188622

Gnomad4 AFR exome AF: 0.550

Gnomad4 AMR exome AF: 0.272

Gnomad4 ASJ exome AF: 0.510

Gnomad4 EAS exome AF: 0.428

Gnomad4 SAS exome AF: 0.509

Gnomad4 FIN exome AF: 0.296

Gnomad4 NFE exome AF: 0.351

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.409 AC: 62118 AN: 151980 Hom.: 13419 Cov.: 32 AF XY: 0.408 AC XY: 30281 AN XY: 74290

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.423

Alfa AF: 0.366 Hom.: 21186

Bravo AF: 0.415

Asia WGS AF: 0.497 AC: 1727 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs583442; hg19: chr5-41586405;