chr9-31837336-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376013	XR_929549.2	n.274+557T>C		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;