rs1275988

Variant names:

• chr2-26691496-C-T
• rs1275988
• ENST00000729046.1:n.108+1434G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000729046.1(ENSG00000295291):​n.108+1434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000295291 ENST00000729046.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 41 publications found

Genes affected

ENSG00000295291 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729046.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295291	ENST00000729046.1		n.108+1434G>A		intron	N/A

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

African (AFR) AF: 0.212 AC: 8785 AN: 41458

American (AMR) AF: 0.648 AC: 9907 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2076 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1260 AN: 5182

South Asian (SAS) AF: 0.542 AC: 2610 AN: 4818

European-Finnish (FIN) AF: 0.528 AC: 5544 AN: 10508

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41478 AN: 67932

Other (OTH) AF: 0.534 AC: 1125 AN: 2108

Alfa AF: 0.507 Hom.: 4163

Bravo AF: 0.482

Asia WGS AF: 0.419 AC: 1460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.0040
DANN	Benign	0.82
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1275988; hg19: chr2-26914364;