rs878855030

Variant names:

• chr6-135411327-AACTGCATAAAATAAA-TTTAAAACTTTAAAAAAGTC
• rs878855030
• NM_001134831.2:c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP6_Moderate

The NM_001134831.2(AHI1):​c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: AHI1 NM_001134831.2 splice_region, intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.63
• Publications: 0 publications found

Genes affected

AHI1 (HGNC:21575): (Abelson helper integration site 1) This gene is apparently required for both cerebellar and cortical development in humans. This gene mutations cause specific forms of Joubert syndrome-related disorders. Joubert syndrome (JS) is a recessively inherited developmental brain disorder with several identified causative chromosomal loci. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]

AHI1 Gene-Disease associations (from GenCC):

• Joubert syndrome 3

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Laboratory for Molecular Medicine, ClinGen, Ambry Genetics
• Joubert syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• Joubert syndrome with ocular defect

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• retinitis pigmentosa

  Inheritance: AR, AD Classification: SUPPORTIVE, LIMITED Submitted by: Ambry Genetics, Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP6: Variant 6-135411327-AACTGCATAAAATAAA-TTTAAAACTTTAAAAAAGTC is Benign according to our data. Variant chr6-135411327-AACTGCATAAAATAAA-TTTAAAACTTTAAAAAAGTC is described in ClinVar as Likely_benign. ClinVar VariationId is 241184.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134831.2. 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
	AHI1	NM_001134831.2	MANE Select	c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	NP_001128303.1	Q8N157-1
	AHI1	NM_001134830.2		c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	NP_001128302.1	Q8N157-1
	AHI1	NM_001350503.2		c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	NP_001337432.1	Q8N157-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1	ENST00000265602.11	TSL:1 MANE Select	c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	ENSP00000265602.6	Q8N157-1
	AHI1	ENST00000367800.8	TSL:1	c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	ENSP00000356774.4	Q8N157-1
	AHI1	ENST00000457866.6	TSL:1	c.2961+6_2961+21delTTTATTTTATGCAGTTinsGACTTTTTTAAAGTTTTAAA		splice_region intron	N/A	ENSP00000388650.2	Q8N157-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Joubert syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs878855030; hg19: chr6-135732465;