rs13403149

Positions:

• chr2-2839536-G-A

Variant summary

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

The XR_001739255.2(LOC105373390):​n.1089+247C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,140 control chromosomes in the GnomAD database, including 8,879 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 0.33 (8879 hom., cov: 33)
• Consequence: LOC105373390 XR_001739255.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

Genes affected

LOC105373390 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373390	XR_001739255.2	n.1089+247C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663497.1	n.730+247C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49834 AN: 152020 Hom.: 8865 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.328 AC: 49878 AN: 152140 Hom.: 8879 Cov.: 33 AF XY: 0.329 AC XY: 24442 AN XY: 74346

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.337

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.361

Alfa AF: 0.385 Hom.: 23346

Bravo AF: 0.323

Asia WGS AF: 0.459 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0090
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13403149; hg19: chr2-2843308;