XR_007095784.1:n.261-16258T>C

Variant names:

• chr3-986665-T-C
• rs4686358
• XR_007095784.1:n.261-16258T>C

Variant summary

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

The XR_007095784.1(LOC107986059):​n.261-16258T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,034 control chromosomes in the GnomAD database, including 51,615 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 0.81 (51615 hom., cov: 31)
• Consequence: LOC107986059 XR_007095784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 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: 0.811 AC: 123145 AN: 151916 Hom.: 51608 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.810 AC: 123192 AN: 152034 Hom.: 51615 Cov.: 31 AF XY: 0.810 AC XY: 60166 AN XY: 74312

African (AFR) AF: 0.597 AC: 24729 AN: 41422

American (AMR) AF: 0.861 AC: 13153 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3022 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3013 AN: 5144

South Asian (SAS) AF: 0.794 AC: 3829 AN: 4824

European-Finnish (FIN) AF: 0.907 AC: 9612 AN: 10594

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.925 AC: 62920 AN: 67992

Other (OTH) AF: 0.832 AC: 1758 AN: 2112

Alfa AF: 0.858 Hom.: 20931

Bravo AF: 0.798

Asia WGS AF: 0.641 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4686358; hg19: chr3-1028349;