rs567992

Positions:

• chr11-106391670-C-T

Variant summary

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

The XR_947985.1(LOC105369474):​n.102-17473C>T 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 0.13 in 152,100 control chromosomes in the GnomAD database, including 1,816 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 0.13 (1816 hom., cov: 32)
• Consequence: LOC105369474 XR_947985.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

LOC105369474 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369474	XR_947985.1	n.102-17473C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19760 AN: 151982 Hom.: 1807 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.130 AC: 19777 AN: 152100 Hom.: 1816 Cov.: 32 AF XY: 0.136 AC XY: 10077 AN XY: 74332

Gnomad4 AFR AF: 0.0288

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.155

Alfa AF: 0.147 Hom.: 2615

Bravo AF: 0.137

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs567992; hg19: chr11-106262397;