XR_001740585.2:n.260+8100A>G

Variant names:

• chr3-965759-A-G
• rs6803398
• XR_001740585.2:n.260+8100A>G

Variant summary

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

The XR_001740585.2(LOC107986059):​n.260+8100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 151,922 control chromosomes in the GnomAD database, including 68,330 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 0.94 (68330 hom., cov: 30)
• Consequence: LOC107986059 XR_001740585.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 0 publications found

Genes affected

LOC107986059 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.945 AC: 143450 AN: 151802 Hom.: 68301 Cov.: 30

Gnomad AFR AF: 0.808

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.998

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.971

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.945 AC: 143535 AN: 151922 Hom.: 68330 Cov.: 30 AF XY: 0.946 AC XY: 70267 AN XY: 74240

African (AFR) AF: 0.808 AC: 33468 AN: 41420

American (AMR) AF: 0.980 AC: 14938 AN: 15238

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3466 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5126 AN: 5126

South Asian (SAS) AF: 0.998 AC: 4806 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10598 AN: 10598

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67911 AN: 67944

Other (OTH) AF: 0.960 AC: 2026 AN: 2110

Alfa AF: 0.967 Hom.: 5487

Bravo AF: 0.938

Asia WGS AF: 0.983 AC: 3419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.0030
DANN	Benign	0.42
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6803398; hg19: chr3-1007443;