rs1671062

Variant names:

• chr11-66514067-A-G
• rs1671062
• NM_024649.5:c.160-339A>G

Variant summary

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

The NM_024649.5(BBS1):​c.160-339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,138 control chromosomes in the GnomAD database, including 33,871 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 0.65 (33871 hom., cov: 32)
• Consequence: BBS1 NM_024649.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 2 publications found

Genes affected

BBS1 (HGNC:966): (Bardet-Biedl syndrome 1) Mutations in this gene have been observed in patients with the major form (type 1) of Bardet-Biedl syndrome. The encoded protein may play a role in eye, limb, cardiac and reproductive system development. [provided by RefSeq, Jul 2008]

BBS1 Gene-Disease associations (from GenCC):

• Bardet-Biedl syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Genomics England PanelApp, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P
• BBS1-related ciliopathy

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

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000256349 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024649.5. 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
	BBS1	NM_024649.5	MANE Select	c.160-339A>G		intron	N/A	NP_078925.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BBS1	ENST00000318312.12	TSL:1 MANE Select	c.160-339A>G		intron	N/A	ENSP00000317469.7	Q8NFJ9-1
	ENSG00000256349	ENST00000419755.3	TSL:2	c.271-339A>G		intron	N/A	ENSP00000398526.3
	BBS1	ENST00000393994.4	TSL:1	c.160-339A>G		intron	N/A	ENSP00000377563.2	Q8NFJ9-3

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99143 AN: 152020 Hom.: 33818 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.652 AC: 99246 AN: 152138 Hom.: 33871 Cov.: 32 AF XY: 0.646 AC XY: 48060 AN XY: 74358

African (AFR) AF: 0.858 AC: 35649 AN: 41534

American (AMR) AF: 0.481 AC: 7342 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2079 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2654 AN: 5166

South Asian (SAS) AF: 0.408 AC: 1966 AN: 4818

European-Finnish (FIN) AF: 0.652 AC: 6904 AN: 10588

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40634 AN: 67966

Other (OTH) AF: 0.623 AC: 1317 AN: 2114

Alfa AF: 0.663 Hom.: 5148

Bravo AF: 0.650

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	8.6
DANN	Benign	0.81
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1671062; hg19: chr11-66281538;