9-108125716-C-G

Variant names:

• chr9-108125716-C-G
• rs662694
• XR_001746881.2:n.721-72422G>C

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-72422G>C 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 151,968 control chromosomes in the GnomAD database, including 29,485 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 (29485 hom., cov: 31)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376214	XR_001746881.2	n.721-72422G>C		intron_variant	Intron 4 of 4
LOC105376214	XR_001746882.2	n.721-72422G>C		intron_variant	Intron 4 of 5
LOC105376214	XR_007061722.1	n.721-72422G>C		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: 93562 AN: 151850 Hom.: 29465 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.839

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.616 AC: 93631 AN: 151968 Hom.: 29485 Cov.: 31 AF XY: 0.626 AC XY: 46484 AN XY: 74282

African (AFR) AF: 0.511 AC: 21167 AN: 41404

American (AMR) AF: 0.644 AC: 9849 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3470

East Asian (EAS) AF: 0.928 AC: 4798 AN: 5168

South Asian (SAS) AF: 0.839 AC: 4042 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6951 AN: 10530

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

European-Non Finnish (NFE) AF: 0.626 AC: 42524 AN: 67964

Other (OTH) AF: 0.629 AC: 1330 AN: 2116

Alfa AF: 0.624 Hom.: 3760

Bravo AF: 0.609

Asia WGS AF: 0.861 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.39
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs662694; hg19: chr9-110887996; COSMIC: COSV60389973;