6-135687470-A-G

Variant names:

• chr6-135687470-A-G
• rs9494332
• ENST00000421378.4:n.419-2153A>G

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.419-2153A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,944 control chromosomes in the GnomAD database, including 7,652 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 0.31 (7652 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 5 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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	NR_026805.1		n.421-2153A>G		intron	N/A
	AHI1-DT	NR_152842.1		n.535-2153A>G		intron	N/A
	AHI1-DT	NR_152844.1		n.535-2153A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.419-2153A>G		intron	N/A
	AHI1-DT	ENST00000579944.1	TSL:2	n.117-2153A>G		intron	N/A
	AHI1-DT	ENST00000653664.1		n.559-2153A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47719 AN: 151826 Hom.: 7641 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.314 AC: 47750 AN: 151944 Hom.: 7652 Cov.: 31 AF XY: 0.311 AC XY: 23105 AN XY: 74248

African (AFR) AF: 0.271 AC: 11220 AN: 41444

American (AMR) AF: 0.352 AC: 5370 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1258 AN: 3464

East Asian (EAS) AF: 0.406 AC: 2086 AN: 5144

South Asian (SAS) AF: 0.411 AC: 1976 AN: 4802

European-Finnish (FIN) AF: 0.198 AC: 2102 AN: 10598

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22656 AN: 67936

Other (OTH) AF: 0.317 AC: 669 AN: 2108

Alfa AF: 0.330 Hom.: 23346

Bravo AF: 0.320

Asia WGS AF: 0.380 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.1
DANN	Benign	0.85
PhyloP100		-0.057

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: rs9494332;

hg19: chr6-136008608;