rs2042762

Variant names:

• chr18-37697659-T-C
• rs2042762
• ENST00000649194.1:n.111-28185T>C

Variant summary

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

The ENST00000649194.1(ENSG00000285940):​n.111-28185T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,304 control chromosomes in the GnomAD database, including 495 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 0.051 (495 hom., cov: 33)
• Consequence: ENSG00000285940 ENST00000649194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 4 publications found

Genes affected

ENSG00000285940 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.186 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
ENSG00000285940	ENST00000649194.1	n.111-28185T>C		intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7707 AN: 152186 Hom.: 492 Cov.: 33

Gnomad AFR AF: 0.0124

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0844

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0506 AC: 7712 AN: 152304 Hom.: 495 Cov.: 33 AF XY: 0.0534 AC XY: 3976 AN XY: 74472

African (AFR) AF: 0.0124 AC: 516 AN: 41586

American (AMR) AF: 0.192 AC: 2931 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3468

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4826

European-Finnish (FIN) AF: 0.0844 AC: 896 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2976 AN: 68012

Other (OTH) AF: 0.0530 AC: 112 AN: 2112

Alfa AF: 0.0497 Hom.: 354

Bravo AF: 0.0614

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2042762; hg19: chr18-35277622;