rs2335092

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000282987 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376988	XR_940646.3	n.545-12238A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000282987	ENST00000634947.1	n.370+25928T>G		intron_variant		5

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

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.491

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2335092; hg19: chr3-21240252;