rs2725236

chr4-87997954-G-Achr4-87997954-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, non coding transcript 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: ENST00000662475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000662475.1	n.113-8402C>T		intron_variant, non_coding_transcript_variant

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;