rs1582861

Positions:

• chr2-136733551-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 0.507 in 151,828 control chromosomes in the GnomAD database, including 19,724 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 0.51 (19724 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.518 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: 0.507 AC: 76874 AN: 151708 Hom.: 19719 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.507 AC: 76906 AN: 151828 Hom.: 19724 Cov.: 31 AF XY: 0.505 AC XY: 37499 AN XY: 74196

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.529

Alfa AF: 0.526 Hom.: 34103

Bravo AF: 0.511

Asia WGS AF: 0.344 AC: 1200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1582861; hg19: chr2-137491121;