rs17006053

Variant names:

• chr4-122708506-C-A
• rs17006053
• XM_011531680.3:c.-11+7940C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-122708506-C-A
• chr4-122708506-C-T

Variant summary

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

The ENST00000660031.2(ENSG00000287692):​n.4232C>A 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 0.242 in 151,908 control chromosomes in the GnomAD database, including 4,688 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 0.24 (4688 hom., cov: 31)
• Consequence: ENSG00000287692 ENST00000660031.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 2 publications found

Genes affected

BBS12 (HGNC:26648): (Bardet-Biedl syndrome 12) The protein encoded by this gene is part of a complex that is involved in membrane trafficking. The encoded protein is a molecular chaperone that aids in protein folding upon ATP hydrolysis. This protein also plays a role in adipocyte differentiation. Defects in this gene are a cause of Bardet-Biedl syndrome type 12. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, May 2010]

BBS12 Gene-Disease associations (from GenCC):

• Bardet-Biedl syndrome 12

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Myriad Women's Health, G2P
• BBS12-related ciliopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• Bardet-Biedl syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000287692 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000660031.2. 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
	ENSG00000287692	ENST00000660031.2		n.4232C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287692	ENST00000755916.1		n.130-4863C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36706 AN: 151790 Hom.: 4685 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.242 AC: 36722 AN: 151908 Hom.: 4688 Cov.: 31 AF XY: 0.240 AC XY: 17801 AN XY: 74224

African (AFR) AF: 0.249 AC: 10288 AN: 41368

American (AMR) AF: 0.249 AC: 3792 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1543 AN: 5166

South Asian (SAS) AF: 0.393 AC: 1890 AN: 4804

European-Finnish (FIN) AF: 0.128 AC: 1355 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15672 AN: 67976

Other (OTH) AF: 0.240 AC: 507 AN: 2110

Alfa AF: 0.130 Hom.: 228

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17006053;

hg19: chr4-123629661;