rs1022298

Positions:

• chr2-103526090-T-G

Variant summary

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

The variant allele was found at a frequency of 0.478 in 152,042 control chromosomes in the GnomAD database, including 18,583 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 0.48 (18583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72655 AN: 151920 Hom.: 18559 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.0195

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.478 AC: 72720 AN: 152042 Hom.: 18583 Cov.: 32 AF XY: 0.471 AC XY: 35030 AN XY: 74318

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.0195

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.477

Alfa AF: 0.457 Hom.: 33191

Bravo AF: 0.477

Asia WGS AF: 0.166 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022298; hg19: chr2-104142548;