11-112166291-G-T

Position:

• chr11-112166291-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The ENST00000527589.1(ENSG00000254638):​n.171-115C>A 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 0.167 in 152,110 control chromosomes in the GnomAD database, including 2,857 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.17 (2857 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000527589.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.824

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 11-112166291-G-T is Benign according to our data. Variant chr11-112166291-G-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987164	XR_001748384.2	n.82-115C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000527589.1	n.171-115C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25385 AN: 151994 Hom.: 2856 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.167 AC: 25383 AN: 152110 Hom.: 2857 Cov.: 32 AF XY: 0.163 AC XY: 12120 AN XY: 74342

Gnomad4 AFR AF: 0.0462

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.00522

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.161

Alfa AF: 0.222 Hom.: 1983

Bravo AF: 0.156

Asia WGS AF: 0.0390 AC: 136 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.35
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5744222; hg19: chr11-112037014;