rs1011108

Positions:

• chr2-26559753-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;