XR_001746668.2:n.302+16369A>T

Variant names:

• chr9-38332793-A-T
• rs716933
• XR_001746668.2:n.302+16369A>T

Variant summary

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

The XR_001746668.2(LOC107987065):​n.302+16369A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,986 control chromosomes in the GnomAD database, including 13,710 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 0.42 (13710 hom., cov: 32)
• Consequence: LOC107987065 XR_001746668.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.456
• Publications: 3 publications found

Genes affected

LOC107987065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.479 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: 0.420 AC: 63726 AN: 151868 Hom.: 13702 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.420 AC: 63761 AN: 151986 Hom.: 13710 Cov.: 32 AF XY: 0.419 AC XY: 31100 AN XY: 74280

African (AFR) AF: 0.315 AC: 13062 AN: 41432

American (AMR) AF: 0.489 AC: 7460 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1450 AN: 3464

East Asian (EAS) AF: 0.390 AC: 2018 AN: 5168

South Asian (SAS) AF: 0.375 AC: 1806 AN: 4816

European-Finnish (FIN) AF: 0.460 AC: 4857 AN: 10562

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31773 AN: 67960

Other (OTH) AF: 0.419 AC: 885 AN: 2112

Alfa AF: 0.436 Hom.: 1819

Bravo AF: 0.416

Asia WGS AF: 0.400 AC: 1392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.085
DANN	Benign	0.82
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs716933; hg19: chr9-38332790; COSMIC: COSV69461047;