rs13403276

Positions:

• chr2-218216574-T-C

Variant summary

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

The XR_923908.2(LOC101928487):​n.437A>G 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 0.0399 in 152,264 control chromosomes in the GnomAD database, including 177 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 0.040 (177 hom., cov: 32)
• Consequence: LOC101928487 XR_923908.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

LOC101928487 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928487	XR_923908.2	n.437A>G		non_coding_transcript_exon_variant	2/2
LOC101928487	XR_241416.3	n.504A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6082 AN: 152146 Hom.: 177 Cov.: 32

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0389

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0374

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0634

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0399 AC: 6077 AN: 152264 Hom.: 177 Cov.: 32 AF XY: 0.0375 AC XY: 2789 AN XY: 74468

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0388

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0374

Gnomad4 NFE AF: 0.0634

Gnomad4 OTH AF: 0.0455

Alfa AF: 0.0596 Hom.: 365

Bravo AF: 0.0388

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	9.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13403276; hg19: chr2-219081297;