rs2768759

chr1-156882671-A-Cchr1-156882671-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;