rs2335092

Variant names:

• chr3-21198760-A-C
• rs2335092
• ENST00000634947.1:n.370+25928T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-21198760-A-C
• chr3-21198760-A-G
• chr3-21198760-A-T

Variant summary

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

The ENST00000634947.1(ENSG00000282987):​n.370+25928T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,708 control chromosomes in the GnomAD database, including 21,586 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 0.51 (21586 hom., cov: 32)
• Consequence: ENSG00000282987 ENST00000634947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

Genes affected

ENSG00000282987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634947.1. 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
	ENSG00000282987	ENST00000634947.1	TSL:5	n.370+25928T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77384 AN: 151588 Hom.: 21558 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.511 AC: 77470 AN: 151708 Hom.: 21586 Cov.: 32 AF XY: 0.522 AC XY: 38671 AN XY: 74116

African (AFR) AF: 0.680 AC: 28154 AN: 41408

American (AMR) AF: 0.581 AC: 8842 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4371 AN: 5170

South Asian (SAS) AF: 0.684 AC: 3295 AN: 4814

European-Finnish (FIN) AF: 0.449 AC: 4725 AN: 10516

Middle Eastern (MID) AF: 0.479 AC: 138 AN: 288

European-Non Finnish (NFE) AF: 0.375 AC: 25433 AN: 67804

Other (OTH) AF: 0.491 AC: 1033 AN: 2104

Alfa AF: 0.438 Hom.: 1928

Bravo AF: 0.528

Asia WGS AF: 0.757 AC: 2627 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.5
DANN	Benign	0.91
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2335092; hg19: chr3-21240252;