6-135508658-T-C

Variant names:

• chr6-135508658-T-C
• rs4896151
• ENST00000421378.4:n.198+10658T>C

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+10658T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,230 control chromosomes in the GnomAD database, including 57,695 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 0.86 (57695 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57
• Publications: 7 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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 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.200+10658T>C		intron	N/A
	AHI1-DT	NR_152842.1		n.314+10141T>C		intron	N/A
	AHI1-DT	NR_152843.1		n.315-9935T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.198+10658T>C		intron	N/A
	AHI1-DT	ENST00000579339.6	TSL:1	n.157-9935T>C		intron	N/A
	AHI1-DT	ENST00000580741.5	TSL:1	n.399+9217T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131293 AN: 152112 Hom.: 57673 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.863 AC: 131372 AN: 152230 Hom.: 57695 Cov.: 32 AF XY: 0.868 AC XY: 64598 AN XY: 74434

African (AFR) AF: 0.674 AC: 27958 AN: 41478

American (AMR) AF: 0.900 AC: 13782 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3319 AN: 3472

East Asian (EAS) AF: 0.957 AC: 4962 AN: 5184

South Asian (SAS) AF: 0.949 AC: 4575 AN: 4822

European-Finnish (FIN) AF: 0.976 AC: 10362 AN: 10612

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63435 AN: 68036

Other (OTH) AF: 0.867 AC: 1832 AN: 2114

Alfa AF: 0.901 Hom.: 130082

Bravo AF: 0.850

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.27
PhyloP100		-2.6

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: rs4896151;

hg19: chr6-135829796;