chr18-37755682-T-C

Variant names:

• chr18-37755682-T-C
• rs972900
• ENST00000649194.1:n.1453+817T>C

Variant summary

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

The ENST00000649194.1(ENSG00000285940):​n.1453+817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,128 control chromosomes in the GnomAD database, including 7,899 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 0.32 (7899 hom., cov: 33)
• Consequence: ENSG00000285940 ENST00000649194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649194.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285940	ENST00000649194.1		n.1453+817T>C		intron	N/A
	ENSG00000306670	ENST00000820022.1		n.348+1054A>G		intron	N/A
	ENSG00000306670	ENST00000820023.1		n.228+9090A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47954 AN: 152010 Hom.: 7887 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.315 AC: 47988 AN: 152128 Hom.: 7899 Cov.: 33 AF XY: 0.323 AC XY: 24022 AN XY: 74338

African (AFR) AF: 0.272 AC: 11279 AN: 41508

American (AMR) AF: 0.388 AC: 5936 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1086 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1593 AN: 5172

South Asian (SAS) AF: 0.467 AC: 2249 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4177 AN: 10582

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20680 AN: 67982

Other (OTH) AF: 0.297 AC: 628 AN: 2112

Alfa AF: 0.310 Hom.: 31402

Bravo AF: 0.312

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs972900; hg19: chr18-35335646;