rs6754521

Variant names:

• chr2-201994894-G-A
• rs6754521

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 0.25 in 151,074 control chromosomes in the GnomAD database, including 5,463 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 0.25 (5463 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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: 0.250 AC: 37715 AN: 150990 Hom.: 5463 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.250 AC: 37715 AN: 151074 Hom.: 5463 Cov.: 30 AF XY: 0.242 AC XY: 17859 AN XY: 73750

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0807

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.275

Alfa AF: 0.297 Hom.: 2710

Bravo AF: 0.245

Asia WGS AF: 0.224 AC: 780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6754521; hg19: chr2-202859617;