rs11032829

Variant names:

• chr11-34726955-T-C
• rs11032829
• ENST00000843048.1:n.507-27503T>C

Variant summary

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

The ENST00000843048.1(ENSG00000309692):​n.507-27503T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,166 control chromosomes in the GnomAD database, including 1,220 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 0.11 (1220 hom., cov: 32)
• Consequence: ENSG00000309692 ENST00000843048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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.507-27503T>C		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.698+24940T>C		intron	N/A
	ENSG00000309692	ENST00000843050.1		n.291-27503T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17454 AN: 152048 Hom.: 1223 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0642

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.115 AC: 17461 AN: 152166 Hom.: 1220 Cov.: 32 AF XY: 0.123 AC XY: 9128 AN XY: 74382

African (AFR) AF: 0.0907 AC: 3765 AN: 41510

American (AMR) AF: 0.0939 AC: 1436 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0642 AC: 223 AN: 3472

East Asian (EAS) AF: 0.343 AC: 1774 AN: 5172

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4816

European-Finnish (FIN) AF: 0.190 AC: 2016 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0989 AC: 6726 AN: 67996

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0988 Hom.: 1408

Bravo AF: 0.104

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11032829; hg19: chr11-34748502;