chr9-108125833-G-A

Variant names:

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.721-72539C>T		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.721-72539C>T		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.721-72539C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;