rs10511887

Positions:

• chr9-31837336-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_929549.2(LOC105376013):​n.274+557T>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

Genes affected

LOC105376013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105376013	XR_929549.2	n.274+557T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0800

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.251

Alfa AF: 0.243 Hom.: 6754

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511887; hg19: chr9-31837334;