rs1011108

Variant names:

• chr2-26559753-C-T
• rs1011108

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.158 AC: 6524 AN: 41404

American (AMR) AF: 0.438 AC: 6677 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1344 AN: 3470

East Asian (EAS) AF: 0.128 AC: 654 AN: 5120

South Asian (SAS) AF: 0.284 AC: 1357 AN: 4778

European-Finnish (FIN) AF: 0.273 AC: 2884 AN: 10548

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24547 AN: 67802

Other (OTH) AF: 0.353 AC: 741 AN: 2098

Alfa AF: 0.332 Hom.: 13193

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
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1011108; hg19: chr2-26782621;