rs2885135

Variant names:

• chr1-13580032-G-C
• rs2885135

Your query was ambiguous. Multiple possible variants found:

• chr1-13580032-G-C
• chr1-13580032-G-T

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 0.225 in 152,182 control chromosomes in the GnomAD database, including 4,329 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 0.22 (4329 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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: 0.224 AC: 34137 AN: 152064 Hom.: 4322 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.225 AC: 34165 AN: 152182 Hom.: 4329 Cov.: 33 AF XY: 0.225 AC XY: 16747 AN XY: 74402

African (AFR) AF: 0.336 AC: 13960 AN: 41524

American (AMR) AF: 0.248 AC: 3788 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3468

East Asian (EAS) AF: 0.0159 AC: 82 AN: 5172

South Asian (SAS) AF: 0.199 AC: 960 AN: 4820

European-Finnish (FIN) AF: 0.200 AC: 2120 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11966 AN: 68004

Other (OTH) AF: 0.219 AC: 463 AN: 2114

Alfa AF: 0.0874 Hom.: 108

Bravo AF: 0.229

Asia WGS AF: 0.124 AC: 436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2885135; hg19: chr1-13906527;