chr4-88004868-C-T

Variant names:

• chr4-88004868-C-T
• rs12511728
• ENST00000662475.1:n.112+3498G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662475.1(ENSG00000286618):​n.112+3498G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,166 control chromosomes in the GnomAD database, including 1,567 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 0.13 (1567 hom., cov: 32)
• Consequence: ENSG00000286618 ENST00000662475.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 4 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286618	ENST00000662475.1		n.112+3498G>A		intron	N/A
	ENSG00000289034	ENST00000779990.1		n.703+1953G>A		intron	N/A
	ENSG00000289034	ENST00000779991.1		n.173-1935G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19578 AN: 152048 Hom.: 1571 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.129 AC: 19599 AN: 152166 Hom.: 1567 Cov.: 32 AF XY: 0.134 AC XY: 10000 AN XY: 74394

African (AFR) AF: 0.157 AC: 6531 AN: 41516

American (AMR) AF: 0.154 AC: 2357 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0819 AC: 284 AN: 3466

East Asian (EAS) AF: 0.407 AC: 2103 AN: 5168

South Asian (SAS) AF: 0.178 AC: 861 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1740 AN: 10572

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5332 AN: 68014

Other (OTH) AF: 0.145 AC: 305 AN: 2106

Alfa AF: 0.101 Hom.: 1164

Bravo AF: 0.134

Asia WGS AF: 0.291 AC: 1010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.19
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs12511728; hg19: chr4-88926020;