rs9321521

Variant names:

• chr6-135668512-G-A
• rs9321521
• ENST00000421378.4:n.283-3782G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421378.4(AHI1-DT):​n.283-3782G>A variant causes a intron 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 ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.285-3782G>A		intron_variant	Intron 2 of 3
AHI1-DT	NR_152842.1	n.399-3782G>A		intron_variant	Intron 3 of 5
AHI1-DT	NR_152844.1	n.399-3782G>A		intron_variant	Intron 3 of 4
AHI1-DT	NR_152845.1	n.523-3782G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.283-3782G>A		intron_variant	Intron 2 of 3	1
AHI1-DT	ENST00000653664.1	n.423-3782G>A		intron_variant	Intron 3 of 4
AHI1-DT	ENST00000655302.1	n.294-3782G>A		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.875 AC: 36041 AN: 41188

American (AMR) AF: 0.462 AC: 6982 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1470 AN: 3462

East Asian (EAS) AF: 0.451 AC: 2294 AN: 5084

South Asian (SAS) AF: 0.503 AC: 2388 AN: 4748

European-Finnish (FIN) AF: 0.204 AC: 2117 AN: 10376

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24468 AN: 67730

Other (OTH) AF: 0.500 AC: 1040 AN: 2080

Alfa AF: 0.410 Hom.: 7057

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
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs9321521; hg19: chr6-135989650;