rs900865

Positions:

• chr11-15708297-C-G

Variant summary

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

The XR_002957240.2(LOC105376567):​n.33G>C 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 152,096 control chromosomes in the GnomAD database, including 21,721 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 (21721 hom., cov: 32)
• Consequence: LOC105376567 XR_002957240.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

LOC105376567 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376567	XR_002957240.2	n.33G>C		non_coding_transcript_exon_variant	1/5
LOC105376567	XR_001748140.2	n.573-3677G>C		intron_variant
LOC105376567	XR_001748141.2	n.260-3677G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254645	ENST00000524613.1	n.448-1203G>C		intron_variant		5
ENSG00000254645	ENST00000663676.1	n.498-1203G>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80442 AN: 151976 Hom.: 21690 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.529 AC: 80524 AN: 152096 Hom.: 21721 Cov.: 32 AF XY: 0.541 AC XY: 40193 AN XY: 74324

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.520

Alfa AF: 0.503 Hom.: 2399

Bravo AF: 0.531

Asia WGS AF: 0.577 AC: 2007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs900865; hg19: chr11-15729843;