rs1534238

Positions:

• chr2-84123793-T-A

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 0.606 in 152,056 control chromosomes in the GnomAD database, including 30,046 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 0.61 (30046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 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

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92122 AN: 151938 Hom.: 30013 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.606 AC: 92209 AN: 152056 Hom.: 30046 Cov.: 32 AF XY: 0.602 AC XY: 44753 AN XY: 74314

Gnomad4 AFR AF: 0.859

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.581

Alfa AF: 0.580 Hom.: 3340

Bravo AF: 0.607

Asia WGS AF: 0.385 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1534238; hg19: chr2-84350917;