5-135902020-G-T

Variant summary

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

The ENST00000523722.1(ENSG00000253927):n.598-1494C>A 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 0.369 in 152,010 control chromosomes in the GnomAD database, including 11,541 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 0.37 (11541 hom., cov: 32)
• Consequence: ENST00000523722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523722.1	n.598-1494C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56045 AN: 151890 Hom.: 11518 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.371

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56104 AN: 152010 Hom.: 11541 Cov.: 32 AF XY: 0.366 AC XY: 27173 AN XY: 74296

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.366

Alfa AF: 0.220 Hom.: 608

Bravo AF: 0.380

Asia WGS AF: 0.300 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.9
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10479109; hg19: chr5-135237709;