rs1453405

Variant names:

• chr2-168451721-T-C
• rs1453405
• XR_002959433.2:n.25091+5310A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-168451721-T-C
• chr2-168451721-T-G

Variant summary

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

The XR_923566.3(LOC102724081):​n.25091+5310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,080 control chromosomes in the GnomAD database, including 12,435 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 0.40 (12432 hom., cov: 32)
  • Exomes 𝑓: 0.38 (3 hom.)
• Consequence: LOC102724081 XR_923566.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502

Genes affected

LOC102724081 (HGNC:):

RN7SL813P (HGNC:46829): (RNA, 7SL, cytoplasmic 813, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724081	XR_002959433.2	n.25091+5310A>G		intron_variant	Intron 1 of 3
LOC102724081	XR_007087285.1	n.25091+5310A>G		intron_variant	Intron 1 of 3
LOC102724081	XR_007087286.1	n.25091+5310A>G		intron_variant	Intron 1 of 3
LOC102724081	XR_923566.3	n.25091+5310A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RN7SL813P	ENST00000489529.3	n.*115T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60040 AN: 151928 Hom.: 12429 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.434

GnomAD4 exome AF: 0.382 AC: 13 AN: 34 Hom.: 3 AF XY: 0.367 AC XY: 11 AN XY: 30

Gnomad4 NFE exome AF: 0.423

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.395 AC: 60060 AN: 152046 Hom.: 12432 Cov.: 32 AF XY: 0.397 AC XY: 29489 AN XY: 74306

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.434

Alfa AF: 0.432 Hom.: 23301

Bravo AF: 0.408

Asia WGS AF: 0.505 AC: 1757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1453405; hg19: chr2-169308231;