rs6759893

Positions:

• chr2-218113757-A-C

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 0.635 in 152,152 control chromosomes in the GnomAD database, including 33,166 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 0.64 (33166 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.902 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: 0.635 AC: 96517 AN: 152034 Hom.: 33103 Cov.: 33

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.635 AC: 96628 AN: 152152 Hom.: 33166 Cov.: 33 AF XY: 0.630 AC XY: 46809 AN XY: 74350

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.649

Alfa AF: 0.593 Hom.: 3506

Bravo AF: 0.654

Asia WGS AF: 0.507 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6759893; hg19: chr2-218978480;