XR_001741711.2:n.204+36904A>G

Variant names:

• chr4-64811729-A-G
• rs1430509
• XR_001741711.2:n.204+36904A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741711.2(LOC107986284):​n.204+36904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 151,092 control chromosomes in the GnomAD database, including 868 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 0.10 (868 hom., cov: 32)
• Consequence: LOC107986284 XR_001741711.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 1 publications found

Genes affected

LOC107986284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15509 AN: 150982 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0753

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.103 AC: 15539 AN: 151092 Hom.: 868 Cov.: 32 AF XY: 0.102 AC XY: 7525 AN XY: 73788

African (AFR) AF: 0.103 AC: 4241 AN: 41144

American (AMR) AF: 0.0817 AC: 1235 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3466

East Asian (EAS) AF: 0.0947 AC: 484 AN: 5110

South Asian (SAS) AF: 0.150 AC: 718 AN: 4782

European-Finnish (FIN) AF: 0.0753 AC: 778 AN: 10338

Middle Eastern (MID) AF: 0.179 AC: 52 AN: 290

European-Non Finnish (NFE) AF: 0.104 AC: 7078 AN: 67832

Other (OTH) AF: 0.118 AC: 248 AN: 2104

Alfa AF: 0.106 Hom.: 498

Bravo AF: 0.100

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.3
DANN	Benign	0.71
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1430509; hg19: chr4-65677447;