rs6545135

Variant names:

• chr2-49825457-C-T
• rs6545135

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 0.356 in 151,920 control chromosomes in the GnomAD database, including 10,385 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 0.36 (10385 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.356 AC: 53992 AN: 151802 Hom.: 10369 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.356 AC: 54052 AN: 151920 Hom.: 10385 Cov.: 32 AF XY: 0.350 AC XY: 25994 AN XY: 74264

African (AFR) AF: 0.496 AC: 20545 AN: 41422

American (AMR) AF: 0.250 AC: 3819 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3468

East Asian (EAS) AF: 0.246 AC: 1269 AN: 5154

South Asian (SAS) AF: 0.415 AC: 2000 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2421 AN: 10540

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21663 AN: 67934

Other (OTH) AF: 0.343 AC: 725 AN: 2112

Alfa AF: 0.334 Hom.: 1128

Bravo AF: 0.359

Asia WGS AF: 0.348 AC: 1211 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	6.8
DANN	Benign	0.72
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6545135; hg19: chr2-50052595;