rs1505846

Variant names:

• chr2-139020712-C-T
• rs1505846

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 0.342 in 152,018 control chromosomes in the GnomAD database, including 10,230 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 0.34 (10230 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 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: 0.342 AC: 51943 AN: 151900 Hom.: 10226 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.342 AC: 51948 AN: 152018 Hom.: 10230 Cov.: 32 AF XY: 0.340 AC XY: 25291 AN XY: 74284

African (AFR) AF: 0.146 AC: 6068 AN: 41506

American (AMR) AF: 0.378 AC: 5775 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3470

East Asian (EAS) AF: 0.281 AC: 1447 AN: 5156

South Asian (SAS) AF: 0.283 AC: 1364 AN: 4824

European-Finnish (FIN) AF: 0.490 AC: 5157 AN: 10516

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29608 AN: 67964

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.406 Hom.: 21745

Bravo AF: 0.328

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1505846; hg19: chr2-139778282;