rs1001862

Variant names:

• chr20-22397838-C-T
• rs1001862
• ENST00000635130.1:n.689-21450G>A

Variant summary

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

The ENST00000635130.1(ENSG00000204684):​n.689-21450G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,192 control chromosomes in the GnomAD database, including 846 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 0.085 (846 hom., cov: 32)
• Consequence: ENSG00000204684 ENST00000635130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 2 publications found

Genes affected

ENSG00000204684 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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
ENSG00000204684	ENST00000635130.1	n.689-21450G>A		intron_variant	Intron 1 of 3	5
ENSG00000204684	ENST00000653586.1	n.868-21450G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12874 AN: 152074 Hom.: 840 Cov.: 32

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0713

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0847 AC: 12897 AN: 152192 Hom.: 846 Cov.: 32 AF XY: 0.0856 AC XY: 6368 AN XY: 74390

African (AFR) AF: 0.0704 AC: 2924 AN: 41528

American (AMR) AF: 0.112 AC: 1704 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2079 AN: 5164

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4830

European-Finnish (FIN) AF: 0.0640 AC: 678 AN: 10598

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0713 AC: 4848 AN: 68012

Other (OTH) AF: 0.0818 AC: 173 AN: 2114

Alfa AF: 0.0923 Hom.: 329

Bravo AF: 0.0922

Asia WGS AF: 0.158 AC: 549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.24
DANN	Benign	0.18
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1001862; hg19: chr20-22378476;