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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373608	XR_007087228.1	n.975G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;