rs9399158

Variant names:

• chr6-135727672-C-T
• rs9399158
• ENST00000655302.1:n.668+11726C>T

Variant summary

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

The ENST00000655302.1(AHI1-DT):​n.668+11726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,008 control chromosomes in the GnomAD database, including 5,871 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 0.26 (5871 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000655302.1	n.668+11726C>T		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.781+37936C>T		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.1	n.507+37936C>T		intron_variant	Intron 4 of 5
AHI1-DT	ENST00000702072.1	n.481+37936C>T		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39737 AN: 151890 Hom.: 5857 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 152008 Hom.: 5871 Cov.: 32 AF XY: 0.259 AC XY: 19220 AN XY: 74278

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.268

Alfa AF: 0.275 Hom.: 762

Bravo AF: 0.268

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399158; hg19: chr6-136048810; COSMIC: COSV70782686;