rs1409470

chr13-104834599-G-Achr13-104834599-G-Cchr13-104834599-G-T

Variant summary

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

The XR_007063861.1(LOC107984607):n.3237G>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 0.609 in 151,880 control chromosomes in the GnomAD database, including 28,488 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 0.61 (28488 hom., cov: 32)
• Consequence: LOC107984607 XR_007063861.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

Genes affected

LOC107984607 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984607	XR_007063861.1	n.3237G>A		non_coding_transcript_exon_variant	3/3
LOC107984606	XR_001749995.2	n.296+2604C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92420 AN: 151764 Hom.: 28481 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.609 AC: 92458 AN: 151880 Hom.: 28488 Cov.: 32 AF XY: 0.619 AC XY: 45986 AN XY: 74252

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.593

Alfa AF: 0.606 Hom.: 12798

Bravo AF: 0.598

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.36
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1409470; hg19: chr13-105486950;