6-135605725-A-G

Variant names:

• chr6-135605725-A-G
• rs4896156
• ENST00000421378.4:n.199-36468A>G

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.199-36468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,094 control chromosomes in the GnomAD database, including 20,878 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 0.49 (20878 hom., cov: 33)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 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.201-36468A>G		intron	N/A
	AHI1-DT	NR_152842.1		n.315-36468A>G		intron	N/A
	AHI1-DT	NR_152844.1		n.315-36468A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.199-36468A>G		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.147-25886A>G		intron	N/A
	AHI1-DT	ENST00000653664.1		n.339-36468A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74966 AN: 151976 Hom.: 20840 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.494 AC: 75060 AN: 152094 Hom.: 20878 Cov.: 33 AF XY: 0.484 AC XY: 35964 AN XY: 74340

African (AFR) AF: 0.775 AC: 32166 AN: 41514

American (AMR) AF: 0.383 AC: 5856 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1442 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1493 AN: 5176

South Asian (SAS) AF: 0.472 AC: 2273 AN: 4816

European-Finnish (FIN) AF: 0.297 AC: 3141 AN: 10568

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27228 AN: 67962

Other (OTH) AF: 0.487 AC: 1026 AN: 2108

Alfa AF: 0.427 Hom.: 19310

Bravo AF: 0.510

Asia WGS AF: 0.419 AC: 1455 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	16
DANN	Benign	0.74
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4896156; hg19: chr6-135926863;