9-31837336-A-G

Variant names:

• chr9-31837336-A-G
• rs10511887
• XR_929549.2:n.274+557T>C

Variant summary

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

The XR_929549.2(LOC105376013):​n.274+557T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,036 control chromosomes in the GnomAD database, including 4,135 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 0.22 (4135 hom., cov: 32)
• Consequence: LOC105376013 XR_929549.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 4 publications found

Genes affected

LOC105376013 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 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: 0.215 AC: 32714 AN: 151918 Hom.: 4129 Cov.: 32

Gnomad AFR AF: 0.0800

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.215 AC: 32733 AN: 152036 Hom.: 4135 Cov.: 32 AF XY: 0.218 AC XY: 16224 AN XY: 74324

African (AFR) AF: 0.0800 AC: 3323 AN: 41524

American (AMR) AF: 0.335 AC: 5113 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1485 AN: 5134

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4818

European-Finnish (FIN) AF: 0.274 AC: 2901 AN: 10584

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17025 AN: 67942

Other (OTH) AF: 0.251 AC: 531 AN: 2114

Alfa AF: 0.241 Hom.: 10030

Bravo AF: 0.214

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.79
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs10511887; hg19: chr9-31837334;