chr6-135662235-A-T

Variant names:

• chr6-135662235-A-T
• rs12196952
• ENST00000421378.4:n.283-10059A>T

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.283-10059A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,874 control chromosomes in the GnomAD database, including 11,220 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 0.37 (11220 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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.285-10059A>T		intron	N/A
	AHI1-DT	NR_152842.1		n.399-10059A>T		intron	N/A
	AHI1-DT	NR_152844.1		n.399-10059A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.283-10059A>T		intron	N/A
	AHI1-DT	ENST00000653664.1		n.423-10059A>T		intron	N/A
	AHI1-DT	ENST00000655302.1		n.294-10059A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56809 AN: 151756 Hom.: 11188 Cov.: 31

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.375 AC: 56877 AN: 151874 Hom.: 11220 Cov.: 31 AF XY: 0.368 AC XY: 27356 AN XY: 74244

African (AFR) AF: 0.511 AC: 21169 AN: 41464

American (AMR) AF: 0.284 AC: 4332 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1301 AN: 3462

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5168

South Asian (SAS) AF: 0.422 AC: 2029 AN: 4806

European-Finnish (FIN) AF: 0.242 AC: 2559 AN: 10558

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22320 AN: 67850

Other (OTH) AF: 0.361 AC: 761 AN: 2108

Alfa AF: 0.359 Hom.: 1264

Bravo AF: 0.381

Asia WGS AF: 0.377 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.97
DANN	Benign	0.66
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs12196952; hg19: chr6-135983373;