rs2725236

Variant names:

• chr4-87997954-G-A
• rs2725236
• ENST00000662475.1:n.113-8402C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-87997954-G-A
• chr4-87997954-G-C
• chr4-87997954-G-T

Variant summary

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

The ENST00000662475.1(ENSG00000286618):​n.113-8402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,752 control chromosomes in the GnomAD database, including 20,218 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 0.51 (20218 hom., cov: 32)
• Consequence: ENSG00000286618 ENST00000662475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

ENSG00000286618 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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
ENSG00000286618	ENST00000662475.1	n.113-8402C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77888 AN: 151634 Hom.: 20194 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.514 AC: 77970 AN: 151752 Hom.: 20218 Cov.: 32 AF XY: 0.517 AC XY: 38378 AN XY: 74162

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.512

Alfa AF: 0.472 Hom.: 34973

Bravo AF: 0.516

Asia WGS AF: 0.554 AC: 1910 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2725236; hg19: chr4-88919106;