rs9494332

chr6-135687470-A-Gchr6-135687470-A-T

Variant summary

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

The NR_152842.1(AHI1-DT):n.535-2153A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,944 control chromosomes in the GnomAD database, including 7,652 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 0.31 (7652 hom., cov: 31)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.535-2153A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.421-2153A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.535-2153A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.659-2153A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.368-2153A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47719 AN: 151826 Hom.: 7641 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.314 AC: 47750 AN: 151944 Hom.: 7652 Cov.: 31 AF XY: 0.311 AC XY: 23105 AN XY: 74248

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.317

Alfa AF: 0.333 Hom.: 14262

Bravo AF: 0.320

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	9.1
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494332; hg19: chr6-136008608;