6-135506428-G-A

Variant names:

• chr6-135506428-G-A
• rs958072
• ENST00000421378.4:n.198+8428G>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+8428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,128 control chromosomes in the GnomAD database, including 47,822 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 0.75 (47822 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.907 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+8428G>A		intron	N/A
	AHI1-DT	NR_152842.1		n.314+7911G>A		intron	N/A
	AHI1-DT	NR_152843.1		n.314+7911G>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+8428G>A		intron	N/A
	AHI1-DT	ENST00000579339.6	TSL:1	n.156+7911G>A		intron	N/A
	AHI1-DT	ENST00000580741.5	TSL:1	n.399+6987G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113776 AN: 152010 Hom.: 47821 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.748 AC: 113807 AN: 152128 Hom.: 47822 Cov.: 32 AF XY: 0.757 AC XY: 56287 AN XY: 74388

African (AFR) AF: 0.325 AC: 13463 AN: 41408

American (AMR) AF: 0.850 AC: 13004 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3264 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4692 AN: 5188

South Asian (SAS) AF: 0.914 AC: 4407 AN: 4824

European-Finnish (FIN) AF: 0.956 AC: 10151 AN: 10620

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62069 AN: 68006

Other (OTH) AF: 0.768 AC: 1624 AN: 2114

Alfa AF: 0.746 Hom.: 7045

Bravo AF: 0.720

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs958072; hg19: chr6-135827566;