4-154592714-T-C

Variant names:

• chr4-154592714-T-C
• rs2070006
• ENST00000819308.1:n.138-214T>C

Variant summary

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

The ENST00000819308.1(ENSG00000306549):​n.138-214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152,036 control chromosomes in the GnomAD database, including 25,737 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 0.58 (25737 hom., cov: 32)
• Consequence: ENSG00000306549 ENST00000819308.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819308.1. 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
	ENSG00000306549	ENST00000819308.1		n.138-214T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87932 AN: 151918 Hom.: 25715 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.579 AC: 87985 AN: 152036 Hom.: 25737 Cov.: 32 AF XY: 0.577 AC XY: 42868 AN XY: 74286

African (AFR) AF: 0.508 AC: 21074 AN: 41464

American (AMR) AF: 0.626 AC: 9570 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5164

South Asian (SAS) AF: 0.555 AC: 2673 AN: 4820

European-Finnish (FIN) AF: 0.541 AC: 5709 AN: 10556

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42029 AN: 67980

Other (OTH) AF: 0.616 AC: 1298 AN: 2108

Alfa AF: 0.605 Hom.: 14770

Bravo AF: 0.581

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.74
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs2070006; hg19: chr4-155513866;