rs10511886

chr9-31836557-T-C

Variant summary

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

The XR_929549.2(LOC105376013):n.361A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,618 control chromosomes in the GnomAD database, including 24,525 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 0.56 (24525 hom., cov: 29)
• Consequence: LOC105376013 XR_929549.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

Genes affected

LOC105376013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376013	XR_929549.2	n.361A>G		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84262 AN: 151500 Hom.: 24511 Cov.: 29

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.556 AC: 84322 AN: 151618 Hom.: 24525 Cov.: 29 AF XY: 0.560 AC XY: 41442 AN XY: 74048

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.587

Alfa AF: 0.626 Hom.: 59390

Bravo AF: 0.536

Asia WGS AF: 0.599 AC: 2082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	3.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511886; hg19: chr9-31836555; COSMIC: COSV60351392;