ENST00000655302.1:n.668+11726C>T

Variant names:

• chr6-135727672-C-T
• rs9399158
• ENST00000655302.1:n.668+11726C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655302.1(AHI1-DT):​n.668+11726C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,008 control chromosomes in the GnomAD database, including 5,871 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 (5871 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655302.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000655302.1		n.668+11726C>T		intron	N/A
	AHI1-DT	ENST00000685995.1		n.781+37936C>T		intron	N/A
	AHI1-DT	ENST00000690403.2		n.507+37936C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39737 AN: 151890 Hom.: 5857 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 152008 Hom.: 5871 Cov.: 32 AF XY: 0.259 AC XY: 19220 AN XY: 74278

African (AFR) AF: 0.145 AC: 6034 AN: 41476

American (AMR) AF: 0.326 AC: 4969 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2344 AN: 5172

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1711 AN: 10536

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20667 AN: 67958

Other (OTH) AF: 0.268 AC: 568 AN: 2116

Alfa AF: 0.269 Hom.: 767

Bravo AF: 0.268

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.15
DANN	Benign	0.43
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9399158; hg19: chr6-136048810; COSMIC: COSV70782686;