rs4526212

chr6-135483493-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134831.2(AHI1):c.135+7130G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,038 control chromosomes in the GnomAD database, including 7,817 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 0.32 (7817 hom., cov: 32)
• Consequence: AHI1 NM_001134831.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1	NM_001134831.2	c.135+7130G>T		intron_variant		ENST00000265602.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1	ENST00000265602.11	c.135+7130G>T		intron_variant		1	NM_001134831.2	P2

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47878 AN: 151920 Hom.: 7814 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.315 AC: 47898 AN: 152038 Hom.: 7817 Cov.: 32 AF XY: 0.313 AC XY: 23286 AN XY: 74324

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.324

Alfa AF: 0.333 Hom.: 1021

Bravo AF: 0.311

Asia WGS AF: 0.320 AC: 1111 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.5
Dann	Benign	0.35

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: rs4526212; hg19: chr6-135804631;