rs2002842

Variant names:

• chr18-78649597-C-A
• rs2002842
• ENST00000759066.1:n.468-3355G>T

Your query was ambiguous. Multiple possible variants found:

• chr18-78649597-C-A
• chr18-78649597-C-G

Variant summary

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

The ENST00000759066.1(ENSG00000298930):​n.468-3355G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,100 control chromosomes in the GnomAD database, including 13,767 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 0.41 (13767 hom., cov: 34)
• Consequence: ENSG00000298930 ENST00000759066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 18 publications found

Genes affected

ENSG00000298930 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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
ENSG00000298930	ENST00000759066.1	n.468-3355G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62583 AN: 151982 Hom.: 13757 Cov.: 34

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.412 AC: 62624 AN: 152100 Hom.: 13767 Cov.: 34 AF XY: 0.421 AC XY: 31279 AN XY: 74384

African (AFR) AF: 0.316 AC: 13123 AN: 41496

American (AMR) AF: 0.501 AC: 7663 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1249 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4242 AN: 5156

South Asian (SAS) AF: 0.468 AC: 2260 AN: 4824

European-Finnish (FIN) AF: 0.419 AC: 4432 AN: 10582

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28410 AN: 67962

Other (OTH) AF: 0.440 AC: 928 AN: 2110

Alfa AF: 0.423 Hom.: 39313

Bravo AF: 0.414

Asia WGS AF: 0.647 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.72
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2002842; hg19: chr18-76409597; COSMIC: COSV58350784;