rs1943218

Variant names:

• chr18-60377199-T-C
• rs1943218
• ENST00000650201.1:n.113+47854T>C

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+47854T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,972 control chromosomes in the GnomAD database, including 7,016 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 0.29 (7016 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824
• Publications: 8 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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
ENSG00000285681	ENST00000650201.1	n.113+47854T>C		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+47854T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43670 AN: 151854 Hom.: 7001 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.288 AC: 43720 AN: 151972 Hom.: 7016 Cov.: 32 AF XY: 0.281 AC XY: 20862 AN XY: 74292

African (AFR) AF: 0.413 AC: 17102 AN: 41386

American (AMR) AF: 0.295 AC: 4507 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 765 AN: 3472

East Asian (EAS) AF: 0.127 AC: 658 AN: 5168

South Asian (SAS) AF: 0.245 AC: 1179 AN: 4818

European-Finnish (FIN) AF: 0.188 AC: 1993 AN: 10584

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16612 AN: 67964

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.268 Hom.: 2640

Bravo AF: 0.306

Asia WGS AF: 0.200 AC: 693 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.80
DANN	Benign	0.73
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1943218; hg19: chr18-58044432;