rs2577256

Positions:

• chr2-11832364-T-C
• chr2-11832364-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_922803.3(LOC105373430):​n.143T>C 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 0.515 in 151,816 control chromosomes in the GnomAD database, including 21,318 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 0.51 (21318 hom., cov: 30)
• Consequence: LOC105373430 XR_922803.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

Genes affected

LOC105373430 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373430	XR_922803.3	n.143T>C		non_coding_transcript_exon_variant	1/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78041 AN: 151698 Hom.: 21274 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.515 AC: 78125 AN: 151816 Hom.: 21318 Cov.: 30 AF XY: 0.506 AC XY: 37556 AN XY: 74190

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.491

Alfa AF: 0.496 Hom.: 19437

Bravo AF: 0.522

Asia WGS AF: 0.269 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2577256; hg19: chr2-11972490;