XR_007063861.1:n.3237G>A

Variant names:

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807560.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304988	ENST00000807560.1		n.286+2604C>T		intron	N/A
	ENSG00000304988	ENST00000807561.1		n.238+2604C>T		intron	N/A

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 v4.9

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;