5-34278321-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286543 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000286543	ENST00000736918.1	n.238-22224T>C		intron_variant	Intron 1 of 1
ENSG00000286543	ENST00000736919.1	n.234-20453T>C		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736920.1	n.128+12515T>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

African (AFR) AF: 0.476 AC: 19720 AN: 41450

American (AMR) AF: 0.932 AC: 14250 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3354 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4555 AN: 5176

South Asian (SAS) AF: 0.940 AC: 4536 AN: 4824

European-Finnish (FIN) AF: 0.902 AC: 9573 AN: 10612

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66101 AN: 68016

Other (OTH) AF: 0.863 AC: 1822 AN: 2112

Alfa AF: 0.887 Hom.: 17169

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4626316; hg19: chr5-34278426;