rs1275988

Positions:

• chr2-26691496-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 0.484 in 151,970 control chromosomes in the GnomAD database, including 20,417 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 0.48 (20417 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26691496C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73553 AN: 151852 Hom.: 20410 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.484 AC: 73585 AN: 151970 Hom.: 20417 Cov.: 33 AF XY: 0.482 AC XY: 35797 AN XY: 74254

Gnomad4 AFR AF: 0.212

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.534

Alfa AF: 0.515 Hom.: 4140

Bravo AF: 0.482

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1275988; hg19: chr2-26914364;