1-2811239-C-T

Variant names:

• chr1-2811239-C-T
• rs10909880

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 0.358 in 152,190 control chromosomes in the GnomAD database, including 11,333 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 0.36 (11333 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.358 AC: 54512 AN: 152072 Hom.: 11326 Cov.: 34

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.358 AC: 54514 AN: 152190 Hom.: 11333 Cov.: 34 AF XY: 0.354 AC XY: 26360 AN XY: 74420

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.404

Alfa AF: 0.445 Hom.: 13621

Bravo AF: 0.357

Asia WGS AF: 0.259 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10909880; hg19: chr1-2727804;