rs11132733

Positions:

• chr4-189720016-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377616	XR_007058514.1	n.3143A>G		non_coding_transcript_exon_variant	1/2
LOC105377616	XR_007058515.1	n.3143A>G		non_coding_transcript_exon_variant	1/2
		n.189720016T>C		intergenic_region

Ensembl

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

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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.707

Alfa AF: 0.788 Hom.: 69831

Bravo AF: 0.661

Asia WGS AF: 0.733 AC: 2548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11132733; hg19: chr4-190641170;