chr18-60392893-C-A

Variant names:

• chr18-60392893-C-A
• rs17773774
• ENST00000650201.1:n.113+63548C>A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000650201.1(ENSG00000285681):​n.113+63548C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,874 control chromosomes in the GnomAD database, including 1,753 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 (1753 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 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+63548C>A		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+63548C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20081 AN: 151758 Hom.: 1752 Cov.: 32

Gnomad AFR AF: 0.0341

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0373

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.132 AC: 20073 AN: 151874 Hom.: 1753 Cov.: 32 AF XY: 0.128 AC XY: 9513 AN XY: 74240

Gnomad4 AFR AF: 0.0339

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0376

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.128

Alfa AF: 0.176 Hom.: 2252

Bravo AF: 0.126

Asia WGS AF: 0.0810 AC: 281 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	14
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17773774; hg19: chr18-58060126;