chr11-34788896-T-C

Variant names:

• chr11-34788896-T-C
• rs10836312
• ENST00000843048.1:n.656+34289T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000843048.1(ENSG00000309692):​n.656+34289T>C variant causes a intron 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: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.822
• Publications: 6 publications found

Genes affected

ENSG00000309692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309692	ENST00000843048.1		n.656+34289T>C		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.848+34289T>C		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.440+34289T>C		intron	N/A

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

African (AFR) AF: 0.410 AC: 16983 AN: 41450

American (AMR) AF: 0.334 AC: 5101 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1132 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2210 AN: 5164

South Asian (SAS) AF: 0.367 AC: 1765 AN: 4812

European-Finnish (FIN) AF: 0.440 AC: 4646 AN: 10550

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28114 AN: 67978

Other (OTH) AF: 0.375 AC: 792 AN: 2112

Alfa AF: 0.400 Hom.: 9972

Bravo AF: 0.395

Asia WGS AF: 0.399 AC: 1385 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Chronic obstructive pulmonary disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10836312; hg19: chr11-34810443;