rs1505846

Positions:

• chr2-139020712-C-T

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 0.342 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.378

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.338

Alfa AF: 0.414 Hom.: 17804

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1505846; hg19: chr2-139778282;