rs10204325

Variant names:

• chr2-76148585-C-T
• rs10204325
• ENST00000670606.1:n.833-58108C>T

Variant summary

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

The ENST00000670606.1(ENSG00000287474):​n.833-58108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,884 control chromosomes in the GnomAD database, including 7,198 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 0.30 (7198 hom., cov: 32)
• Consequence: ENSG00000287474 ENST00000670606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

ENSG00000287474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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
ENSG00000287474	ENST00000670606.1	n.833-58108C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45813 AN: 151766 Hom.: 7202 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.302 AC: 45810 AN: 151884 Hom.: 7198 Cov.: 32 AF XY: 0.299 AC XY: 22220 AN XY: 74234

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.313

Alfa AF: 0.332 Hom.: 14650

Bravo AF: 0.296

Asia WGS AF: 0.295 AC: 1026 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10204325; hg19: chr2-76375711;