18-61695285-C-T

Variant names:

• chr18-61695285-C-T
• rs7231234
• ENST00000590199.6:n.538-2012G>A

Variant summary

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

The ENST00000590199.6(ENSG00000267175):​n.538-2012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,076 control chromosomes in the GnomAD database, including 13,831 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 0.37 (13831 hom., cov: 33)
• Consequence: ENSG00000267175 ENST00000590199.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 3 publications found

Genes affected

ENSG00000267175 (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 = 0.706 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
ENSG00000267175	ENST00000590199.6	n.538-2012G>A		intron_variant	Intron 2 of 3	3
ENSG00000267175	ENST00000590968.1	n.234-2012G>A		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55467 AN: 151958 Hom.: 13789 Cov.: 33

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.365 AC: 55571 AN: 152076 Hom.: 13831 Cov.: 33 AF XY: 0.362 AC XY: 26890 AN XY: 74358

African (AFR) AF: 0.713 AC: 29576 AN: 41478

American (AMR) AF: 0.269 AC: 4109 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3464

East Asian (EAS) AF: 0.345 AC: 1786 AN: 5170

South Asian (SAS) AF: 0.355 AC: 1710 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2079 AN: 10572

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.218 AC: 14829 AN: 67980

Other (OTH) AF: 0.316 AC: 667 AN: 2108

Alfa AF: 0.161 Hom.: 389

Bravo AF: 0.385

Asia WGS AF: 0.383 AC: 1331 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.32
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs7231234; hg19: chr18-59362518;