5-34276810-G-C

Variant names:

• chr5-34276810-G-C
• rs7701604
• ENST00000658746.1:n.136-9200G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658746.1(ENSG00000286543):​n.136-9200G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,080 control chromosomes in the GnomAD database, including 55,834 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 0.83 (55834 hom., cov: 30)
• Consequence: ENSG00000286543 ENST00000658746.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• 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=-1.08).
• 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.136-9200G>C		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736918.1	n.238-23735G>C		intron_variant	Intron 1 of 1
ENSG00000286543	ENST00000736919.1	n.234-21964G>C		intron_variant	Intron 1 of 2
ENSG00000286543	ENST00000736920.1	n.128+11004G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126801 AN: 151962 Hom.: 55822 Cov.: 30

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.834 AC: 126848 AN: 152080 Hom.: 55834 Cov.: 30 AF XY: 0.836 AC XY: 62104 AN XY: 74328

African (AFR) AF: 0.518 AC: 21459 AN: 41408

American (AMR) AF: 0.937 AC: 14328 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4557 AN: 5178

South Asian (SAS) AF: 0.941 AC: 4539 AN: 4826

European-Finnish (FIN) AF: 0.903 AC: 9563 AN: 10594

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

European-Non Finnish (NFE) AF: 0.972 AC: 66103 AN: 67996

Other (OTH) AF: 0.873 AC: 1844 AN: 2112

Alfa AF: 0.888 Hom.: 7715

Bravo AF: 0.821

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.053
DANN	Benign	0.40
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7701604; hg19: chr5-34276915;