6-135530435-G-A

Variant names:

• chr6-135530435-G-A
• rs9494266
• ENST00000421378.4:n.198+32435G>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.198+32435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,068 control chromosomes in the GnomAD database, including 10,614 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 (10614 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 13 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421378.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	NR_026805.1		n.200+32435G>A		intron	N/A
	AHI1-DT	NR_152842.1		n.314+31918G>A		intron	N/A
	AHI1-DT	NR_152843.1		n.552+11605G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.198+32435G>A		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.146+31918G>A		intron	N/A
	AHI1-DT	ENST00000653664.1		n.338+11605G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39012 AN: 151950 Hom.: 10578 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0598

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.257 AC: 39109 AN: 152068 Hom.: 10614 Cov.: 32 AF XY: 0.249 AC XY: 18488 AN XY: 74364

African (AFR) AF: 0.693 AC: 28724 AN: 41438

American (AMR) AF: 0.150 AC: 2287 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0598 AC: 207 AN: 3464

East Asian (EAS) AF: 0.0961 AC: 497 AN: 5174

South Asian (SAS) AF: 0.0865 AC: 417 AN: 4822

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10612

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0873 AC: 5937 AN: 67986

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.135 Hom.: 13911

Bravo AF: 0.285

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.62
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs9494266; hg19: chr6-135851573;