18-60392296-C-T

Variant names:

• chr18-60392296-C-T
• rs7240064
• ENST00000650201.1:n.113+62951C>T

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+62951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,144 control chromosomes in the GnomAD database, including 1,732 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 0.13 (1732 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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+62951C>T		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+62951C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19926 AN: 152026 Hom.: 1731 Cov.: 32

Gnomad AFR AF: 0.0333

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0376

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.131 AC: 19919 AN: 152144 Hom.: 1732 Cov.: 32 AF XY: 0.127 AC XY: 9465 AN XY: 74366

African (AFR) AF: 0.0332 AC: 1377 AN: 41538

American (AMR) AF: 0.122 AC: 1857 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 460 AN: 3472

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5176

South Asian (SAS) AF: 0.161 AC: 775 AN: 4828

European-Finnish (FIN) AF: 0.159 AC: 1684 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13029 AN: 67974

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.0745 Hom.: 123

Bravo AF: 0.125

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.072
DANN	Benign	0.15
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7240064; hg19: chr18-58059529;