rs9389316

Positions:

• chr6-135679865-C-A
• chr6-135679865-C-T

Variant summary

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

The NR_152842.1(AHI1-DT):​n.534+7436C>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 0.116 in 151,668 control chromosomes in the GnomAD database, including 2,287 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 0.12 (2287 hom., cov: 30)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.534+7436C>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.420+7436C>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.534+7436C>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.658+7436C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.367+7436C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17499 AN: 151556 Hom.: 2279 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.0724

Gnomad FIN AF: 0.00653

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.116 AC: 17547 AN: 151668 Hom.: 2287 Cov.: 30 AF XY: 0.112 AC XY: 8327 AN XY: 74098

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.0788

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.0725

Gnomad4 FIN AF: 0.00653

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.111

Alfa AF: 0.0414 Hom.: 447

Bravo AF: 0.131

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9389316; hg19: chr6-136001003;