rs1893146

Variant names:

• chr18-8987429-G-A
• rs1893146
• ENST00000827768.1:n.267-3968C>T

Your query was ambiguous. Multiple possible variants found:

• chr18-8987429-G-A
• chr18-8987429-G-T

Variant summary

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

The ENST00000827768.1(ENSG00000288939):​n.267-3968C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,158 control chromosomes in the GnomAD database, including 1,267 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 (1267 hom., cov: 33)
• Consequence: ENSG00000288939 ENST00000827768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.42
• Publications: 6 publications found

Genes affected

ENSG00000288939 (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 (EAS) allele frequency at 95% confidence interval = 0.289 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
ENSG00000288939	ENST00000827768.1	n.267-3968C>T		intron_variant	Intron 2 of 3
ENSG00000286765	ENST00000828045.1	n.478-8631G>A		intron_variant	Intron 1 of 2
ENSG00000286765	ENST00000828046.1	n.194-3988G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18563 AN: 152040 Hom.: 1265 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0986

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.122 AC: 18582 AN: 152158 Hom.: 1267 Cov.: 33 AF XY: 0.124 AC XY: 9210 AN XY: 74388

African (AFR) AF: 0.112 AC: 4639 AN: 41510

American (AMR) AF: 0.0984 AC: 1506 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 349 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1555 AN: 5160

South Asian (SAS) AF: 0.151 AC: 726 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1104 AN: 10584

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8341 AN: 67992

Other (OTH) AF: 0.138 AC: 292 AN: 2114

Alfa AF: 0.111 Hom.: 1432

Bravo AF: 0.119

Asia WGS AF: 0.217 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.012
DANN	Benign	0.53
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1893146; hg19: chr18-8987427;