rs9483869

Variant names:

• chr6-135701776-T-C
• rs9483869
• ENST00000579944.1:n.230+12040T>C

Variant summary

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

The ENST00000579944.1(AHI1-DT):​n.230+12040T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0989 in 152,096 control chromosomes in the GnomAD database, including 2,087 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 0.099 (2087 hom., cov: 32)
• Consequence: AHI1-DT ENST00000579944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 2 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579944.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	NR_152842.1		n.648+12040T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000579944.1	TSL:2	n.230+12040T>C		intron	N/A
	AHI1-DT	ENST00000655302.1		n.543+12040T>C		intron	N/A
	AHI1-DT	ENST00000685995.1		n.781+12040T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0986 AC: 14979 AN: 151978 Hom.: 2070 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0989 AC: 15043 AN: 152096 Hom.: 2087 Cov.: 32 AF XY: 0.0962 AC XY: 7151 AN XY: 74348

African (AFR) AF: 0.316 AC: 13074 AN: 41416

American (AMR) AF: 0.0469 AC: 717 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4824

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0109 AC: 742 AN: 68006

Other (OTH) AF: 0.0866 AC: 183 AN: 2112

Alfa AF: 0.0592 Hom.: 416

Bravo AF: 0.112

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.29
PhyloP100		-1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9483869;

hg19: chr6-136022914;