5-135899917-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

Genes affected

ENSG00000254239 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0714 AC: 1 AN: 14

American (AMR) AF: 0.333 AC: 2 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.286 AC: 4 AN: 14

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.192 AC: 5 AN: 26

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 6

European-Non Finnish (NFE) AF: 0.122 AC: 32 AN: 262

Other (OTH) AF: 0.0714 AC: 2 AN: 28

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

African (AFR) AF: 0.128 AC: 5316 AN: 41524

American (AMR) AF: 0.177 AC: 2707 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3472

East Asian (EAS) AF: 0.157 AC: 814 AN: 5172

South Asian (SAS) AF: 0.0960 AC: 463 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1667 AN: 10608

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9125 AN: 67986

Other (OTH) AF: 0.114 AC: 241 AN: 2116

Alfa AF: 0.129 Hom.: 2564

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
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs31563; hg19: chr5-135235606;