5-41587260-T-C

Position:

• chr5-41587260-T-C

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.528A>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 0.173 in 412,810 control chromosomes in the GnomAD database, including 7,350 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 0.19 (3276 hom., cov: 33)
  • Exomes 𝑓: 0.16 (4074 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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.528A>G		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29070 AN: 152114 Hom.: 3271 Cov.: 33

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00484

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.162 AC: 42156 AN: 260578 Hom.: 4074 Cov.: 0 AF XY: 0.163 AC XY: 23760 AN XY: 145518

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.134

Gnomad4 ASJ exome AF: 0.291

Gnomad4 EAS exome AF: 0.00371

Gnomad4 SAS exome AF: 0.161

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.169

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.191 AC: 29080 AN: 152232 Hom.: 3276 Cov.: 33 AF XY: 0.185 AC XY: 13802 AN XY: 74438

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.00485

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0809

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.205

Alfa AF: 0.172 Hom.: 1150

Bravo AF: 0.205

Asia WGS AF: 0.0910 AC: 316 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs598318; hg19: chr5-41587362;