chr6-135539276-G-A

Variant names:

• chr6-135539276-G-A
• rs12203875
• ENST00000421378.4:n.198+41276G>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+41276G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,924 control chromosomes in the GnomAD database, including 17,760 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 0.44 (17760 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.565 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+41276G>A		intron	N/A
	AHI1-DT	NR_152842.1		n.314+40759G>A		intron	N/A
	AHI1-DT	NR_152843.1		n.553-15752G>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+41276G>A		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.146+40759G>A		intron	N/A
	AHI1-DT	ENST00000653664.1		n.338+20446G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66881 AN: 151806 Hom.: 17762 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.440 AC: 66879 AN: 151924 Hom.: 17760 Cov.: 31 AF XY: 0.450 AC XY: 33396 AN XY: 74242

African (AFR) AF: 0.120 AC: 4984 AN: 41432

American (AMR) AF: 0.536 AC: 8181 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1990 AN: 3468

East Asian (EAS) AF: 0.582 AC: 2998 AN: 5152

South Asian (SAS) AF: 0.497 AC: 2390 AN: 4806

European-Finnish (FIN) AF: 0.663 AC: 7002 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37612 AN: 67940

Other (OTH) AF: 0.444 AC: 939 AN: 2114

Alfa AF: 0.496 Hom.: 9695

Bravo AF: 0.418

Asia WGS AF: 0.505 AC: 1756 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	0.66
DANN	Benign	0.25
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs12203875; hg19: chr6-135860414;