5-135899917-C-T

Position:

• chr5-135899917-C-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, non coding transcript 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: ENST00000522973.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.948

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000522973.1	n.116-35C>T		intron_variant, non_coding_transcript_variant		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;