ENST00000687402.2:n.195+25703C>T

Variant names:

• chr2-62322149-C-T
• rs4672503
• ENST00000687402.2:n.195+25703C>T

Variant summary

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

The ENST00000687402.2(ENSG00000228541):​n.195+25703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,034 control chromosomes in the GnomAD database, including 8,577 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 0.33 (8577 hom., cov: 32)
• Consequence: ENSG00000228541 ENST00000687402.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 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
ENSG00000228541	ENST00000687402.2	n.195+25703C>T		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000687773.2	n.199+25703C>T		intron_variant	Intron 1 of 1
ENSG00000228541	ENST00000688476.2	n.202-23765C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49428 AN: 151916 Hom.: 8584 Cov.: 32

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.325 AC: 49432 AN: 152034 Hom.: 8577 Cov.: 32 AF XY: 0.320 AC XY: 23811 AN XY: 74302

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.271

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.326

Alfa AF: 0.289 Hom.: 8864

Bravo AF: 0.340

Asia WGS AF: 0.348 AC: 1207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	8.1
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4672503; hg19: chr2-62549284;