11-34788896-T-C

Position:

• chr11-34788896-T-C

Variant summary

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

The XR_007062652.1(LOC102723568):​n.1044+34289T>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 0.403 in 152,002 control chromosomes in the GnomAD database, including 12,472 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.40 (12472 hom., cov: 31)
• Consequence: LOC102723568 XR_007062652.1 intron, non_coding_transcript
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.822

Genes affected

LOC102723568 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723568	XR_007062652.1	n.1044+34289T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61231 AN: 151884 Hom.: 12461 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.403 AC: 61271 AN: 152002 Hom.: 12472 Cov.: 31 AF XY: 0.402 AC XY: 29847 AN XY: 74282

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.375

Alfa AF: 0.401 Hom.: 8348

Bravo AF: 0.395

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Chronic obstructive pulmonary disease Other:1

association, no assertion criteria provided

case-control

HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas

Feb 03, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10836312; hg19: chr11-34810443;