ENST00000421378.4:n.198+21918C>A

Variant names:

• chr6-135519918-C-A
• rs9647635
• ENST00000421378.4:n.198+21918C>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+21918C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 151,886 control chromosomes in the GnomAD database, including 37,601 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 0.70 (37601 hom., cov: 30)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 17 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 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+21918C>A		intron	N/A
	AHI1-DT	NR_152842.1		n.314+21401C>A		intron	N/A
	AHI1-DT	NR_152843.1		n.552+1088C>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+21918C>A		intron	N/A
	AHI1-DT	ENST00000579339.6	TSL:1	n.394+1088C>A		intron	N/A
	AHI1-DT	ENST00000436554.5	TSL:5	n.398-974C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106127 AN: 151768 Hom.: 37556 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.699 AC: 106226 AN: 151886 Hom.: 37601 Cov.: 30 AF XY: 0.701 AC XY: 51990 AN XY: 74210

African (AFR) AF: 0.821 AC: 34040 AN: 41440

American (AMR) AF: 0.688 AC: 10481 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2205 AN: 3468

East Asian (EAS) AF: 0.677 AC: 3491 AN: 5156

South Asian (SAS) AF: 0.585 AC: 2816 AN: 4810

European-Finnish (FIN) AF: 0.706 AC: 7442 AN: 10538

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43463 AN: 67934

Other (OTH) AF: 0.683 AC: 1437 AN: 2104

Alfa AF: 0.698 Hom.: 5508

Bravo AF: 0.706

Asia WGS AF: 0.678 AC: 2360 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	0.080
DANN	Benign	0.28
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs9647635; hg19: chr6-135841056; COSMIC: COSV69848620;