rs1671062

chr11-66514067-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BBS1	NM_024649.5	c.160-339A>G		intron_variant		ENST00000318312.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BBS1	ENST00000318312.12	c.160-339A>G		intron_variant		1	NM_024649.5	P1

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

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.623

Alfa AF: 0.656 Hom.: 4873

Bravo AF: 0.650

Asia WGS AF: 0.502 AC: 1747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	8.6
Dann	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs1671062; hg19: chr11-66281538;