rs899102

Variant names:

• chr18-55788098-A-G
• rs899102
• ENST00000589662.1:n.365-515A>G

Variant summary

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

The ENST00000589662.1(ENSG00000267284):​n.365-515A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,038 control chromosomes in the GnomAD database, including 15,328 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 0.44 (15328 hom., cov: 32)
• Consequence: ENSG00000267284 ENST00000589662.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 4 publications found

Genes affected

ENSG00000267284 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372130	XR_007066382.1	n.476-515A>G		intron_variant	Intron 4 of 8
LOC105372130	XR_007066383.1	n.1171-515A>G		intron_variant	Intron 1 of 4
LOC105372130	XR_935487.3	n.1242-515A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267284	ENST00000589662.1	n.365-515A>G		intron_variant	Intron 3 of 3	5
ENSG00000267284	ENST00000654829.1	n.304-515A>G		intron_variant	Intron 4 of 8
ENSG00000267284	ENST00000729561.1	n.548-515A>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67227 AN: 151920 Hom.: 15305 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.443 AC: 67292 AN: 152038 Hom.: 15328 Cov.: 32 AF XY: 0.438 AC XY: 32534 AN XY: 74306

African (AFR) AF: 0.508 AC: 21062 AN: 41446

American (AMR) AF: 0.514 AC: 7857 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1283 AN: 3462

East Asian (EAS) AF: 0.199 AC: 1033 AN: 5178

South Asian (SAS) AF: 0.252 AC: 1218 AN: 4826

European-Finnish (FIN) AF: 0.368 AC: 3884 AN: 10546

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.435 AC: 29544 AN: 67978

Other (OTH) AF: 0.443 AC: 934 AN: 2108

Alfa AF: 0.438 Hom.: 46981

Bravo AF: 0.459

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.9
DANN	Benign	0.61
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs899102; hg19: chr18-53455329;