12-64759540-GGGGCGGAGAACCGGAGAAAA-G

Position:

• chr12-64759540-GGGGCGGAGAACCGGAGAAAA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001330187.2(TBC1D30):​c.-430_-411del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0503 in 457,844 control chromosomes in the GnomAD database, including 2,078 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.078 (926 hom., cov: 30)
  • Exomes 𝑓: 0.037 (1152 hom.)
• Consequence: TBC1D30 NM_001330187.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.36

Genes affected

TBC1D30 (HGNC:29164): (TBC1 domain family member 30) Enables GTPase activator activity and small GTPase binding activity. Involved in negative regulation of cilium assembly and positive regulation of GTPase activity. Located in ciliary basal body; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-64759540-GGGGCGGAGAACCGGAGAAAA-G is Benign according to our data. Variant chr12-64759540-GGGGCGGAGAACCGGAGAAAA-G is described in ClinVar as [Benign]. Clinvar id is 1287064.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D30	NM_001330187.2	c.-430_-411del		5_prime_UTR_variant	1/14		NP_001317116.1
TBC1D30	XM_024448903.2	c.-1793_-1774del		5_prime_UTR_variant	1/14		XP_024304671.1
TBC1D30	XM_024448904.2	c.-408_-389del		5_prime_UTR_variant	1/14		XP_024304672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D30	ENST00000674237.1	c.-430_-411del		5_prime_UTR_variant	1/14			ENSP00000501371
TBC1D30	ENST00000434563.3	n.75_94del		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11609 AN: 149416 Hom.: 921 Cov.: 30

Gnomad AFR AF: 0.0380

Gnomad AMI AF: 0.0884

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0438

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.0619

GnomAD4 exome AF: 0.0369 AC: 11391 AN: 308310 Hom.: 1152 AF XY: 0.0353 AC XY: 5633 AN XY: 159580

Gnomad4 AFR exome AF: 0.0166

Gnomad4 AMR exome AF: 0.0847

Gnomad4 ASJ exome AF: 0.0199

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.0362

Gnomad4 FIN exome AF: 0.0458

Gnomad4 NFE exome AF: 0.0282

Gnomad4 OTH exome AF: 0.0354

GnomAD4 genome AF: 0.0777 AC: 11622 AN: 149534 Hom.: 926 Cov.: 30 AF XY: 0.0797 AC XY: 5804 AN XY: 72826

Gnomad4 AFR AF: 0.0383

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0438

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.0631

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0717

Gnomad4 OTH AF: 0.0627

Alfa AF: 0.0717 Hom.: 46

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1275976175; hg19: chr12-65153320;