rs1293344

Positions:

• chr11-112166661-A-G

Variant summary

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

The ENST00000527589.1(ENSG00000254638):​n.171-485T>C 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 0.257 in 152,034 control chromosomes in the GnomAD database, including 5,201 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 0.26 (5201 hom., cov: 32)
• Consequence: ENST00000527589.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987164	XR_001748384.2	n.81+402T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000527589.1	n.171-485T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39121 AN: 151914 Hom.: 5202 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.257 AC: 39114 AN: 152034 Hom.: 5201 Cov.: 32 AF XY: 0.258 AC XY: 19177 AN XY: 74292

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.253

Alfa AF: 0.267 Hom.: 2597

Bravo AF: 0.259

Asia WGS AF: 0.193 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.31

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: rs1293344; hg19: chr11-112037384;