rs1011108

Variant names:

• chr2-26559753-C-T
• rs1011108

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 0.297 in 151,682 control chromosomes in the GnomAD database, including 7,474 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 0.30 (7474 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.979

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.297 AC: 45031 AN: 151566 Hom.: 7473 Cov.: 30

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.297 AC: 45037 AN: 151682 Hom.: 7474 Cov.: 30 AF XY: 0.296 AC XY: 21902 AN XY: 74108

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.353

Alfa AF: 0.334 Hom.: 1595

Bravo AF: 0.302

Asia WGS AF: 0.198 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.49
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011108; hg19: chr2-26782621;