ENST00000655302.1:n.668+43380A>G

Variant names:

• chr6-135759326-A-G
• rs9399161
• ENST00000655302.1:n.668+43380A>G

Variant summary

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

The ENST00000655302.1(AHI1-DT):​n.668+43380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,048 control chromosomes in the GnomAD database, including 15,774 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 0.43 (15774 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 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+43380A>G		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.782-17412A>G		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.1	n.508-50521A>G		intron_variant	Intron 4 of 5
AHI1-DT	ENST00000702072.1	n.482-50521A>G		intron_variant	Intron 4 of 7

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65786 AN: 151930 Hom.: 15723 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.433 AC: 65894 AN: 152048 Hom.: 15774 Cov.: 32 AF XY: 0.428 AC XY: 31782 AN XY: 74336

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.421

Alfa AF: 0.358 Hom.: 20160

Bravo AF: 0.453

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399161; hg19: chr6-136080464; COSMIC: COSV69427681;