rs1316268

Variant names:

• chr9-91972280-A-G
• rs1316268
• XR_930124.1:n.363-5604T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-91972280-A-G
• chr9-91972280-A-T

Variant summary

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

The XR_930124.1(LOC105376148):​n.363-5604T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,916 control chromosomes in the GnomAD database, including 22,669 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 0.52 (22669 hom., cov: 31)
• Consequence: LOC105376148 XR_930124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 5 publications found

Genes affected

LOC105376148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 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: 0.515 AC: 78195 AN: 151798 Hom.: 22624 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.515 AC: 78302 AN: 151916 Hom.: 22669 Cov.: 31 AF XY: 0.516 AC XY: 38312 AN XY: 74232

African (AFR) AF: 0.790 AC: 32731 AN: 41438

American (AMR) AF: 0.560 AC: 8542 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3468

East Asian (EAS) AF: 0.427 AC: 2196 AN: 5146

South Asian (SAS) AF: 0.448 AC: 2144 AN: 4786

European-Finnish (FIN) AF: 0.378 AC: 3988 AN: 10556

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25569 AN: 67952

Other (OTH) AF: 0.483 AC: 1017 AN: 2106

Alfa AF: 0.462 Hom.: 2925

Bravo AF: 0.540

Asia WGS AF: 0.484 AC: 1687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.22
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1316268; hg19: chr9-94734562;