18-60350016-T-C

Variant names:

• chr18-60350016-T-C
• rs11152221
• ENST00000650201.1:n.113+20671T>C

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+20671T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,942 control chromosomes in the GnomAD database, including 31,523 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 0.63 (31523 hom., cov: 31)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 8 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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+20671T>C		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+20671T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95780 AN: 151824 Hom.: 31507 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.631 AC: 95829 AN: 151942 Hom.: 31523 Cov.: 31 AF XY: 0.641 AC XY: 47613 AN XY: 74270

African (AFR) AF: 0.434 AC: 17956 AN: 41386

American (AMR) AF: 0.713 AC: 10870 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3466

East Asian (EAS) AF: 0.900 AC: 4646 AN: 5164

South Asian (SAS) AF: 0.670 AC: 3226 AN: 4818

European-Finnish (FIN) AF: 0.729 AC: 7714 AN: 10576

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46487 AN: 67968

Other (OTH) AF: 0.676 AC: 1426 AN: 2108

Alfa AF: 0.673 Hom.: 57831

Bravo AF: 0.618

Asia WGS AF: 0.773 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11152221; hg19: chr18-58017249;