rs471467

Variant names:

• chr9-108125833-G-A
• rs471467
• XR_001746881.2:n.721-72539C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-108125833-G-A
• chr9-108125833-G-C
• chr9-108125833-G-T

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-72539C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 151,966 control chromosomes in the GnomAD database, including 29,502 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 0.62 (29502 hom., cov: 31)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393
• Publications: 10 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 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: 0.616 AC: 93584 AN: 151848 Hom.: 29481 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.616 AC: 93654 AN: 151966 Hom.: 29502 Cov.: 31 AF XY: 0.626 AC XY: 46497 AN XY: 74270

African (AFR) AF: 0.511 AC: 21190 AN: 41444

American (AMR) AF: 0.644 AC: 9831 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2188 AN: 3462

East Asian (EAS) AF: 0.929 AC: 4803 AN: 5170

South Asian (SAS) AF: 0.841 AC: 4053 AN: 4818

European-Finnish (FIN) AF: 0.661 AC: 6973 AN: 10552

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42509 AN: 67938

Other (OTH) AF: 0.628 AC: 1327 AN: 2112

Alfa AF: 0.627 Hom.: 14643

Bravo AF: 0.609

Asia WGS AF: 0.861 AC: 2992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.40
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs471467; hg19: chr9-110888113; COSMIC: COSV60389979;