rs11132733

Variant names:

• chr4-189720016-T-C
• rs11132733
• XR_007058514.1:n.3143A>G

Variant summary

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

The XR_007058514.1(LOC105377616):​n.3143A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,074 control chromosomes in the GnomAD database, including 38,192 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 0.68 (38192 hom., cov: 32)
• Consequence: LOC105377616 XR_007058514.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 8 publications found

Genes affected

LOC105377616 (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 (NFE) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808166.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305047	ENST00000808166.1		n.346+1190A>G		intron	N/A
	ENSG00000305047	ENST00000808167.1		n.310+1190A>G		intron	N/A
	ENSG00000305047	ENST00000808168.1		n.299+1190A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103285 AN: 151956 Hom.: 38192 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.679 AC: 103306 AN: 152074 Hom.: 38192 Cov.: 32 AF XY: 0.681 AC XY: 50635 AN XY: 74344

African (AFR) AF: 0.358 AC: 14833 AN: 41450

American (AMR) AF: 0.739 AC: 11290 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2882 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4091 AN: 5162

South Asian (SAS) AF: 0.795 AC: 3832 AN: 4818

European-Finnish (FIN) AF: 0.814 AC: 8617 AN: 10582

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55336 AN: 67998

Other (OTH) AF: 0.707 AC: 1487 AN: 2102

Alfa AF: 0.768 Hom.: 172353

Bravo AF: 0.661

Asia WGS AF: 0.733 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.17
DANN	Benign	0.18
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11132733; hg19: chr4-190641170;