5-8328670-G-T

Variant names:

• chr5-8328670-G-T
• rs925203
• ENST00000654773.1:n.261+37507C>A

Variant summary

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

The ENST00000654773.1(ENSG00000288002):​n.261+37507C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,652 control chromosomes in the GnomAD database, including 4,671 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 0.24 (4671 hom., cov: 31)
• Consequence: ENSG00000288002 ENST00000654773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

ENSG00000288002 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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
ENSG00000288002	ENST00000654773.1	n.261+37507C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36056 AN: 151536 Hom.: 4662 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.276

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.238 AC: 36098 AN: 151652 Hom.: 4671 Cov.: 31 AF XY: 0.242 AC XY: 17930 AN XY: 74102

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.270

Alfa AF: 0.221 Hom.: 7922

Bravo AF: 0.245

Asia WGS AF: 0.429 AC: 1490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925203; hg19: chr5-8328783;