5-34278321-T-C

Variant names:

• chr5-34278321-T-C
• rs4626316
• ENST00000658746.1:n.136-7689T>C

Variant summary

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

The ENST00000658746.1(ENSG00000286543):​n.136-7689T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,158 control chromosomes in the GnomAD database, including 54,851 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 0.82 (54851 hom., cov: 31)
• Consequence: ENSG00000286543 ENST00000658746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

Genes affected

ENSG00000286543 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 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
ENSG00000286543	ENST00000658746.1	n.136-7689T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124966 AN: 152040 Hom.: 54843 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.940

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.822 AC: 125008 AN: 152158 Hom.: 54851 Cov.: 31 AF XY: 0.823 AC XY: 61255 AN XY: 74392

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.932

Gnomad4 ASJ AF: 0.967

Gnomad4 EAS AF: 0.880

Gnomad4 SAS AF: 0.940

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.863

Alfa AF: 0.901 Hom.: 15753

Bravo AF: 0.807

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.21
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4626316; hg19: chr5-34278426;