4-180038549-C-T

Variant names:

• chr4-180038549-C-T
• rs2309123
• ENST00000663768.1:n.504-17158G>A

Variant summary

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

The ENST00000663768.1(ENSG00000287083):​n.504-17158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,030 control chromosomes in the GnomAD database, including 7,922 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 0.26 (7922 hom., cov: 32)
• Consequence: ENSG00000287083 ENST00000663768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

Genes affected

ENSG00000287083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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
ENSG00000287083	ENST00000663768.1	n.504-17158G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39836 AN: 151912 Hom.: 7896 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.263 AC: 39923 AN: 152030 Hom.: 7922 Cov.: 32 AF XY: 0.265 AC XY: 19703 AN XY: 74308

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.243

Alfa AF: 0.0807 Hom.: 142

Bravo AF: 0.287

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2309123; hg19: chr4-180959702;