rs1943217

Variant names:

• chr18-60376948-T-G
• rs1943217
• ENST00000650201.1:n.113+47603T>G

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+47603T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,976 control chromosomes in the GnomAD database, including 14,182 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 0.40 (14182 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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+47603T>G		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+47603T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59975 AN: 151858 Hom.: 14152 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.395 AC: 60051 AN: 151976 Hom.: 14182 Cov.: 32 AF XY: 0.387 AC XY: 28762 AN XY: 74288

African (AFR) AF: 0.657 AC: 27172 AN: 41378

American (AMR) AF: 0.350 AC: 5342 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3468

East Asian (EAS) AF: 0.136 AC: 706 AN: 5180

South Asian (SAS) AF: 0.286 AC: 1379 AN: 4818

European-Finnish (FIN) AF: 0.269 AC: 2852 AN: 10584

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20511 AN: 67958

Other (OTH) AF: 0.358 AC: 757 AN: 2112

Alfa AF: 0.351 Hom.: 4941

Bravo AF: 0.417

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1943217; hg19: chr18-58044181;