rs6754952

Variant names:

• chr2-231516534-A-C
• rs6754952

Your query was ambiguous. Multiple possible variants found:

• chr2-231516534-A-C
• chr2-231516534-A-G

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 0.569 in 151,956 control chromosomes in the GnomAD database, including 25,023 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 0.57 (25023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 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: 0.569 AC: 86362 AN: 151838 Hom.: 24986 Cov.: 31

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.569 AC: 86439 AN: 151956 Hom.: 25023 Cov.: 31 AF XY: 0.573 AC XY: 42509 AN XY: 74240

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.608

Alfa AF: 0.588 Hom.: 54278

Bravo AF: 0.569

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6754952; hg19: chr2-232381245;