rs599176

Positions:

• chr5-41587464-A-T

Variant summary

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

The ENST00000504215.1(ENSG00000251478):​n.324T>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 0.0925 in 636,414 control chromosomes in the GnomAD database, including 3,964 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 (965 hom., cov: 33)
  • Exomes 𝑓: 0.089 (2999 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• 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.324T>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15675 AN: 152136 Hom.: 963 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0892 AC: 43165 AN: 484160 Hom.: 2999 Cov.: 0 AF XY: 0.0885 AC XY: 23711 AN XY: 268030

Gnomad4 AFR exome AF: 0.201

Gnomad4 AMR exome AF: 0.0831

Gnomad4 ASJ exome AF: 0.138

Gnomad4 EAS exome AF: 0.00702

Gnomad4 SAS exome AF: 0.0794

Gnomad4 FIN exome AF: 0.0583

Gnomad4 NFE exome AF: 0.0931

Gnomad4 OTH exome AF: 0.103

GnomAD4 genome AF: 0.103 AC: 15678 AN: 152254 Hom.: 965 Cov.: 33 AF XY: 0.100 AC XY: 7460 AN XY: 74452

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.00406

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.109

Alfa AF: 0.100 Hom.: 111

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	1.5
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599176; hg19: chr5-41587566;