chr18-60497226-T-C

Variant names:

• chr18-60497226-T-C
• rs582970
• ENST00000650201.1:n.215+17554T>C

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.215+17554T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,004 control chromosomes in the GnomAD database, including 14,099 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 0.43 (14099 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650201.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285681	ENST00000650201.1		n.215+17554T>C		intron	N/A
	ENSG00000285681	ENST00000658928.1		n.258+17554T>C		intron	N/A
	ENSG00000285681	ENST00000667405.1		n.128+17554T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64611 AN: 151886 Hom.: 14077 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.425 AC: 64676 AN: 152004 Hom.: 14099 Cov.: 32 AF XY: 0.425 AC XY: 31587 AN XY: 74288

African (AFR) AF: 0.517 AC: 21420 AN: 41444

American (AMR) AF: 0.350 AC: 5346 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1566 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1795 AN: 5184

South Asian (SAS) AF: 0.473 AC: 2281 AN: 4820

European-Finnish (FIN) AF: 0.449 AC: 4721 AN: 10522

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26280 AN: 67952

Other (OTH) AF: 0.398 AC: 841 AN: 2112

Alfa AF: 0.308 Hom.: 947

Bravo AF: 0.420

Asia WGS AF: 0.412 AC: 1431 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.1
DANN	Benign	0.73
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs582970; hg19: chr18-58164459;