4-87997954-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

Genes affected

ENSG00000286618 (HGNC:):

ENSG00000289034 (HGNC:58844):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662475.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286618	ENST00000662475.1		n.113-8402C>T		intron	N/A
	ENSG00000289034	ENST00000779990.1		n.929-471C>T		intron	N/A
	ENSG00000289034	ENST00000779991.1		n.507-471C>T		intron	N/A

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

African (AFR) AF: 0.540 AC: 22349 AN: 41368

American (AMR) AF: 0.571 AC: 8722 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3440 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1987 AN: 4820

European-Finnish (FIN) AF: 0.565 AC: 5911 AN: 10468

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32555 AN: 67870

Other (OTH) AF: 0.512 AC: 1082 AN: 2114

Alfa AF: 0.481 Hom.: 52867

Bravo AF: 0.516

Asia WGS AF: 0.554 AC: 1910 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.4
DANN	Benign	0.50
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs2725236; hg19: chr4-88919106;