rs1409470

Variant names:

• chr13-104834599-G-A
• rs1409470
• XR_007063861.1:n.3237G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-104834599-G-A
• chr13-104834599-G-C
• chr13-104834599-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC107984607 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984607	XR_007063861.1	n.3237G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC107984606	XR_001749993.2	n.296+2604C>T		intron_variant	Intron 2 of 3
LOC107984606	XR_001749994.2	n.296+2604C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304988	ENST00000807560.1	n.286+2604C>T		intron_variant	Intron 2 of 3
ENSG00000304988	ENST00000807561.1	n.238+2604C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.533 AC: 22049 AN: 41400

American (AMR) AF: 0.667 AC: 10160 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1796 AN: 3472

East Asian (EAS) AF: 0.811 AC: 4184 AN: 5156

South Asian (SAS) AF: 0.682 AC: 3292 AN: 4824

European-Finnish (FIN) AF: 0.746 AC: 7876 AN: 10558

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41210 AN: 67930

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.605 Hom.: 14290

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
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1409470; hg19: chr13-105486950;