rs9787877

chr11-69229042-T-C

Variant summary

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

The XR_007062756.1(LOC105369367):n.2482A>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 0.529 in 149,968 control chromosomes in the GnomAD database, including 22,207 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 0.53 (22207 hom., cov: 30)
• Consequence: LOC105369367 XR_007062756.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

Genes affected

LOC105369367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369367	XR_007062756.1	n.2482A>G		non_coding_transcript_exon_variant	5/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.529 AC: 79215 AN: 149844 Hom.: 22170 Cov.: 30

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.0754

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.529 AC: 79305 AN: 149968 Hom.: 22207 Cov.: 30 AF XY: 0.521 AC XY: 38125 AN XY: 73162

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.539

Alfa AF: 0.495 Hom.: 6686

Bravo AF: 0.527

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9787877; hg19: chr11-68996509;