5-41587183-G-T

Position:

• chr5-41587183-G-T

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.605C>A 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 0.1 in 244,222 control chromosomes in the GnomAD database, including 1,449 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 0.10 (964 hom., cov: 33)
  • Exomes 𝑓: 0.096 (485 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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.605C>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15663 AN: 152066 Hom.: 962 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0636

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0958 AC: 8814 AN: 92038 Hom.: 485 Cov.: 0 AF XY: 0.0969 AC XY: 4866 AN XY: 50228

Gnomad4 AFR exome AF: 0.245

Gnomad4 AMR exome AF: 0.0945

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.00447

Gnomad4 SAS exome AF: 0.104

Gnomad4 FIN exome AF: 0.0617

Gnomad4 NFE exome AF: 0.0963

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.103 AC: 15666 AN: 152184 Hom.: 964 Cov.: 33 AF XY: 0.100 AC XY: 7457 AN XY: 74404

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00407

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0550 Hom.: 62

Bravo AF: 0.111

Asia WGS AF: 0.0500 AC: 174 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.93
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs650073; hg19: chr5-41587285;