9-114560262-A-G

Variant names:

• chr9-114560262-A-G
• rs10817638
• XR_930260.2:n.201-1521T>C

Variant summary

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

The XR_930260.2(LOC105376229):​n.201-1521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,116 control chromosomes in the GnomAD database, including 10,519 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 0.37 (10519 hom., cov: 32)
• Consequence: LOC105376229 XR_930260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34
• Publications: 13 publications found

Genes affected

LOC105376229 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 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: 0.370 AC: 56245 AN: 151998 Hom.: 10511 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.370 AC: 56268 AN: 152116 Hom.: 10519 Cov.: 32 AF XY: 0.370 AC XY: 27504 AN XY: 74338

African (AFR) AF: 0.371 AC: 15371 AN: 41480

American (AMR) AF: 0.460 AC: 7028 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2084 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4820

European-Finnish (FIN) AF: 0.329 AC: 3485 AN: 10590

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24220 AN: 68008

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.367 Hom.: 31374

Bravo AF: 0.381

Asia WGS AF: 0.366 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs10817638; hg19: chr9-117322542;