5-131948917-C-T

Variant summary

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

The ENST00000446275.1(ENSG00000234758):n.117+4393C>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 0.353 in 151,996 control chromosomes in the GnomAD database, including 11,185 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 0.35 (11185 hom., cov: 32)
• Consequence: ENST00000446275.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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
	ENST00000446275.1	n.117+4393C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53638 AN: 151880 Hom.: 11154 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.353 AC: 53721 AN: 151996 Hom.: 11185 Cov.: 32 AF XY: 0.354 AC XY: 26272 AN XY: 74272

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.314

Alfa AF: 0.269 Hom.: 3072

Bravo AF: 0.368

Asia WGS AF: 0.384 AC: 1336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.094
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs477086; hg19: chr5-131284610;