5-135899917-C-T

Variant names:

• chr5-135899917-C-T
• rs31563
• ENST00000522973.1:n.116-35C>T

Variant summary

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

The ENST00000522973.1(ENSG00000254239):​n.116-35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,564 control chromosomes in the GnomAD database, including 1,482 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 0.14 (1480 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: ENSG00000254239 ENST00000522973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

Genes affected

ENSG00000254239 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254239	ENST00000522973.1	n.116-35C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20670 AN: 152084 Hom.: 1486 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0959

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.116

GnomAD4 exome AF: 0.127 AC: 46 AN: 362 Hom.: 2 Cov.: 0 AF XY: 0.120 AC XY: 33 AN XY: 274

Gnomad4 AFR exome AF: 0.0714

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.286

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.0714

GnomAD4 genome AF: 0.136 AC: 20669 AN: 152202 Hom.: 1480 Cov.: 32 AF XY: 0.137 AC XY: 10225 AN XY: 74436

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.114

Alfa AF: 0.126 Hom.: 1817

Bravo AF: 0.140

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.069
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31563; hg19: chr5-135235606;