rs11603288

chr11-69229315-G-Achr11-69229315-G-C

Variant summary

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

The XR_007062756.1(LOC105369367):n.2209C>T 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 0.151 in 152,294 control chromosomes in the GnomAD database, including 2,248 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 0.15 (2248 hom., cov: 33)
• Consequence: LOC105369367 XR_007062756.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678

Genes affected

LOC105369367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369367	XR_007062756.1	n.2209C>T		non_coding_transcript_exon_variant	5/5

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22981 AN: 152176 Hom.: 2250 Cov.: 33

Gnomad AFR AF: 0.0417

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.151 AC: 22982 AN: 152294 Hom.: 2248 Cov.: 33 AF XY: 0.145 AC XY: 10772 AN XY: 74468

Gnomad4 AFR AF: 0.0416

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0260

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.177

Alfa AF: 0.189 Hom.: 902

Bravo AF: 0.154

Asia WGS AF: 0.0730 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.6
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11603288; hg19: chr11-68996782;