rs10204325

chr2-76148585-C-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, non coding transcript 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: ENST00000670606.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670606.1	n.833-58108C>T		intron_variant, non_coding_transcript_variant

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;