rs9821892

Variant names:

• chr3-119773102-A-T
• rs9821892
• ENST00000648112.1:c.*1+22004A>T

Variant summary

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

The ENST00000648112.1(ENSG00000285585):​c.*1+22004A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,710 control chromosomes in the GnomAD database, including 12,375 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 0.35 (12375 hom., cov: 32)
• Consequence: ENSG00000285585 ENST00000648112.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 2 publications found

Genes affected

ENSG00000285585 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648112.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285585	ENST00000648112.1		c.*1+22004A>T		intron	N/A	ENSP00000497876.1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53533 AN: 151594 Hom.: 12344 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.353 AC: 53611 AN: 151710 Hom.: 12375 Cov.: 32 AF XY: 0.352 AC XY: 26108 AN XY: 74114

African (AFR) AF: 0.665 AC: 27506 AN: 41346

American (AMR) AF: 0.311 AC: 4742 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3466

East Asian (EAS) AF: 0.213 AC: 1098 AN: 5154

South Asian (SAS) AF: 0.286 AC: 1374 AN: 4800

European-Finnish (FIN) AF: 0.245 AC: 2561 AN: 10440

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14418 AN: 67926

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.318 Hom.: 931

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9821892; hg19: chr3-119491949;