18-60441957-C-T

Variant names:

• chr18-60441957-C-T
• rs4257308
• ENST00000650201.1:n.114-37614C>T

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.114-37614C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,110 control chromosomes in the GnomAD database, including 39,737 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 0.71 (39737 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 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.114-37614C>T		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.157-37614C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107771 AN: 151992 Hom.: 39691 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.709 AC: 107875 AN: 152110 Hom.: 39737 Cov.: 32 AF XY: 0.710 AC XY: 52799 AN XY: 74332

African (AFR) AF: 0.896 AC: 37243 AN: 41546

American (AMR) AF: 0.672 AC: 10261 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1966 AN: 3460

East Asian (EAS) AF: 0.953 AC: 4936 AN: 5180

South Asian (SAS) AF: 0.682 AC: 3288 AN: 4824

European-Finnish (FIN) AF: 0.594 AC: 6261 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41812 AN: 67974

Other (OTH) AF: 0.684 AC: 1446 AN: 2114

Alfa AF: 0.648 Hom.: 94212

Bravo AF: 0.725

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.5
DANN	Benign	0.87
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4257308; hg19: chr18-58109190;