chr9-108193008-G-A

Variant names:

• chr9-108193008-G-A
• rs556399
• XR_001746881.2:n.720+117658C>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.720+117658C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,948 control chromosomes in the GnomAD database, including 15,094 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 (15094 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 8 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 = 0.897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63251 AN: 151830 Hom.: 15085 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.416 AC: 63280 AN: 151948 Hom.: 15094 Cov.: 32 AF XY: 0.429 AC XY: 31884 AN XY: 74262

African (AFR) AF: 0.211 AC: 8745 AN: 41462

American (AMR) AF: 0.480 AC: 7337 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4738 AN: 5154

South Asian (SAS) AF: 0.636 AC: 3061 AN: 4810

European-Finnish (FIN) AF: 0.554 AC: 5832 AN: 10530

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.451 AC: 30665 AN: 67934

Other (OTH) AF: 0.425 AC: 897 AN: 2112

Alfa AF: 0.447 Hom.: 34026

Bravo AF: 0.406

Asia WGS AF: 0.733 AC: 2544 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.55
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs556399; hg19: chr9-110955288;