chr2-127431732-C-T

Position:

• chr2-127431732-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105373608 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105373608	XR_007087228.1	n.975G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.687

Alfa AF: 0.685 Hom.: 33894

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1401296; hg19: chr2-128189308;