chr18-29149852-T-A

Variant names:

• chr18-29149852-T-A
• rs1972603
• ENST00000789716.1:n.272+7114A>T

Variant summary

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

The ENST00000789716.1(ENSG00000302813):​n.272+7114A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,580 control chromosomes in the GnomAD database, including 18,660 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 0.46 (18660 hom., cov: 31)
• Consequence: ENSG00000302813 ENST00000789716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 2 publications found

Genes affected

ENSG00000302813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789716.1. 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
	ENSG00000302813	ENST00000789716.1		n.272+7114A>T		intron	N/A
	LINC02879	ENST00000789904.1		n.58+3479T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69041 AN: 151462 Hom.: 18652 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.456 AC: 69069 AN: 151580 Hom.: 18660 Cov.: 31 AF XY: 0.452 AC XY: 33504 AN XY: 74046

African (AFR) AF: 0.148 AC: 6132 AN: 41424

American (AMR) AF: 0.534 AC: 8103 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2183 AN: 3460

East Asian (EAS) AF: 0.512 AC: 2609 AN: 5098

South Asian (SAS) AF: 0.473 AC: 2279 AN: 4818

European-Finnish (FIN) AF: 0.467 AC: 4922 AN: 10534

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40887 AN: 67750

Other (OTH) AF: 0.556 AC: 1170 AN: 2106

Alfa AF: 0.512 Hom.: 2662

Bravo AF: 0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.53
DANN	Benign	0.50
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs1972603; hg19: chr18-26729817;