rs9399161

Positions:

• chr6-135759326-A-G
• chr6-135759326-A-T

Variant summary

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

The ENST00000702072.1(AHI1-DT):​n.482-50521A>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 0.433 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 ENST00000702072.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.482-50521A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000655302.1	n.668+43380A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000685995.1	n.782-17412A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000690403.1	n.508-50521A>G		intron_variant, non_coding_transcript_variant

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;