rs2768759

Variant names:

• chr1-156882671-A-C
• rs2768759

Your query was ambiguous. Multiple possible variants found:

• chr1-156882671-A-C
• chr1-156882671-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 0.524 in 151,998 control chromosomes in the GnomAD database, including 25,984 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 0.52 (25984 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 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: 0.524 AC: 79586 AN: 151878 Hom.: 25984 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.524 AC: 79592 AN: 151998 Hom.: 25984 Cov.: 32 AF XY: 0.518 AC XY: 38453 AN XY: 74284

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.0549

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.730

Gnomad4 OTH AF: 0.551

Alfa AF: 0.525 Hom.: 3607

Bravo AF: 0.500

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2768759; hg19: chr1-156852463;