chr18-77242359-A-G

Variant names:

• chr18-77242359-A-G
• rs1893829
• ENST00000844037.1:n.162+8489T>C

Variant summary

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

The ENST00000844037.1(ENSG00000309801):​n.162+8489T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 152,002 control chromosomes in the GnomAD database, including 42,157 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 0.74 (42157 hom., cov: 31)
• Consequence: ENSG00000309801 ENST00000844037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 publications found

Genes affected

ENSG00000309801 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844037.1. 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
	ENSG00000309801	ENST00000844037.1		n.162+8489T>C		intron	N/A
	ENSG00000309801	ENST00000844038.1		n.118+8442T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112459 AN: 151884 Hom.: 42120 Cov.: 31

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.740 AC: 112545 AN: 152002 Hom.: 42157 Cov.: 31 AF XY: 0.738 AC XY: 54855 AN XY: 74318

African (AFR) AF: 0.753 AC: 31189 AN: 41432

American (AMR) AF: 0.653 AC: 9976 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3191 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2992 AN: 5172

South Asian (SAS) AF: 0.671 AC: 3222 AN: 4804

European-Finnish (FIN) AF: 0.729 AC: 7696 AN: 10550

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51854 AN: 67982

Other (OTH) AF: 0.773 AC: 1634 AN: 2114

Alfa AF: 0.761 Hom.: 127950

Bravo AF: 0.739

Asia WGS AF: 0.652 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1893829; hg19: chr18-74954315;