rs1401296

Variant names:

• chr2-127431732-C-T
• rs1401296
• XR_007087228.1:n.975G>A

Variant summary

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

The XR_007087228.1(LOC105373608):​n.975G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 152,162 control chromosomes in the GnomAD database, including 37,287 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 0.70 (37287 hom., cov: 33)
• Consequence: LOC105373608 XR_007087228.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 16 publications found

Genes affected

LOC105373608 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106177 AN: 152042 Hom.: 37279 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.698 AC: 106222 AN: 152162 Hom.: 37287 Cov.: 33 AF XY: 0.695 AC XY: 51653 AN XY: 74374

African (AFR) AF: 0.750 AC: 31163 AN: 41524

American (AMR) AF: 0.752 AC: 11500 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2377 AN: 3472

East Asian (EAS) AF: 0.588 AC: 3039 AN: 5164

South Asian (SAS) AF: 0.518 AC: 2498 AN: 4826

European-Finnish (FIN) AF: 0.673 AC: 7126 AN: 10584

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.679 AC: 46147 AN: 67988

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.686 Hom.: 41206

Bravo AF: 0.711

Asia WGS AF: 0.550 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs1401296; hg19: chr2-128189308;