6-135679865-C-A

Variant names:

• chr6-135679865-C-A
• rs9389316
• ENST00000421378.4:n.418+7436C>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.418+7436C>A variant causes a intron 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 ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 7 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=-0.92).
• 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 rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.420+7436C>A		intron_variant	Intron 3 of 3
AHI1-DT	NR_152842.1	n.534+7436C>A		intron_variant	Intron 4 of 5
AHI1-DT	NR_152844.1	n.534+7436C>A		intron_variant	Intron 4 of 4
AHI1-DT	NR_152845.1	n.658+7436C>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.418+7436C>A		intron_variant	Intron 3 of 3	1
AHI1-DT	ENST00000579944.1	n.116+7436C>A		intron_variant	Intron 1 of 2	2
AHI1-DT	ENST00000653664.1	n.558+7436C>A		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.326 AC: 13425 AN: 41186

American (AMR) AF: 0.0788 AC: 1197 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.0508 AC: 263 AN: 5180

South Asian (SAS) AF: 0.0725 AC: 348 AN: 4800

European-Finnish (FIN) AF: 0.00653 AC: 69 AN: 10562

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0285 AC: 1935 AN: 67962

Other (OTH) AF: 0.111 AC: 233 AN: 2106

Alfa AF: 0.0550 Hom.: 2435

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs9389316; hg19: chr6-136001003;