chr18-77168012-G-A

Variant names:

• chr18-77168012-G-A
• rs1789139
• ENST00000843890.1:n.300+5130G>A

Variant summary

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

The ENST00000843890.1(ENSG00000265844):​n.300+5130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,188 control chromosomes in the GnomAD database, including 1,101 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 0.12 (1101 hom., cov: 33)
• Consequence: ENSG00000265844 ENST00000843890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 2 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843890.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000265844	ENST00000843890.1		n.300+5130G>A		intron	N/A
	ENSG00000309823	ENST00000844124.1		n.243+745C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17865 AN: 152070 Hom.: 1087 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0822

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.118 AC: 17928 AN: 152188 Hom.: 1101 Cov.: 33 AF XY: 0.118 AC XY: 8761 AN XY: 74402

African (AFR) AF: 0.147 AC: 6088 AN: 41508

American (AMR) AF: 0.118 AC: 1801 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.0826 AC: 428 AN: 5180

South Asian (SAS) AF: 0.0873 AC: 422 AN: 4832

European-Finnish (FIN) AF: 0.110 AC: 1169 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7473 AN: 68002

Other (OTH) AF: 0.126 AC: 266 AN: 2106

Alfa AF: 0.105 Hom.: 446

Bravo AF: 0.117

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1789139; hg19: chr18-74879968;