rs9321521

chr6-135668512-G-A

Variant summary

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

The NR_152842.1(AHI1-DT):n.399-3782G>A 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 0.512 in 150,964 control chromosomes in the GnomAD database, including 23,839 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 0.51 (23839 hom., cov: 28)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.867 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.399-3782G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.285-3782G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.399-3782G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.523-3782G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.232-3782G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77141 AN: 150848 Hom.: 23774 Cov.: 28

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.512 AC: 77265 AN: 150964 Hom.: 23839 Cov.: 28 AF XY: 0.503 AC XY: 37009 AN XY: 73636

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.500

Alfa AF: 0.408 Hom.: 6179

Bravo AF: 0.544

Asia WGS AF: 0.496 AC: 1724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	3.2
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9321521; hg19: chr6-135989650;