4-154592124-C-T

Variant names:

• chr4-154592124-C-T
• rs2070008
• ENST00000819308.1:n.138-804C>T

Variant summary

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

The ENST00000819308.1(ENSG00000306549):​n.138-804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,086 control chromosomes in the GnomAD database, including 58,744 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 0.88 (58744 hom., cov: 30)
• Consequence: ENSG00000306549 ENST00000819308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 3 publications found

Genes affected

ENSG00000306549 (HGNC:):

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 = 0.922 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
ENSG00000306549	ENST00000819308.1	n.138-804C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133595 AN: 151970 Hom.: 58700 Cov.: 30

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.889

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

GnomAD4 genome AF: 0.879 AC: 133695 AN: 152086 Hom.: 58744 Cov.: 30 AF XY: 0.878 AC XY: 65251 AN XY: 74328

African (AFR) AF: 0.893 AC: 37031 AN: 41472

American (AMR) AF: 0.876 AC: 13392 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2950 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4882 AN: 5170

South Asian (SAS) AF: 0.857 AC: 4133 AN: 4820

European-Finnish (FIN) AF: 0.853 AC: 9009 AN: 10566

Middle Eastern (MID) AF: 0.908 AC: 265 AN: 292

European-Non Finnish (NFE) AF: 0.873 AC: 59354 AN: 67988

Other (OTH) AF: 0.888 AC: 1874 AN: 2110

Alfa AF: 0.878 Hom.: 20742

Bravo AF: 0.882

Asia WGS AF: 0.891 AC: 3098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.13
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2070008; hg19: chr4-155513276;