rs1534238

Variant names:

• chr2-84123793-T-A
• rs1534238

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.859 AC: 35642 AN: 41498

American (AMR) AF: 0.467 AC: 7136 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1984 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1691 AN: 5162

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4818

European-Finnish (FIN) AF: 0.608 AC: 6414 AN: 10558

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.523 AC: 35550 AN: 67962

Other (OTH) AF: 0.581 AC: 1227 AN: 2112

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
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs1534238; hg19: chr2-84350917;