rs1001862

chr20-22397838-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635130.1(ENSG00000204684):n.689-21450G>A variant causes a intron, non coding transcript 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: ENST00000635130.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000635130.1	n.689-21450G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000653586.1	n.868-21450G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.0640

Gnomad4 NFE AF: 0.0713

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0758 Hom.: 74

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001862; hg19: chr20-22378476;