6-135615740-G-A

Variant names:

• chr6-135615740-G-A
• rs6925684
• ENST00000421378.4:n.199-26453G>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.199-26453G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 152,062 control chromosomes in the GnomAD database, including 17,869 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 0.46 (17869 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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.201-26453G>A		intron	N/A
	AHI1-DT	NR_152842.1		n.315-26453G>A		intron	N/A
	AHI1-DT	NR_152844.1		n.315-26453G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000421378.4	TSL:1	n.199-26453G>A		intron	N/A
	AHI1-DT	ENST00000438618.2	TSL:3	n.147-15871G>A		intron	N/A
	AHI1-DT	ENST00000653664.1		n.339-26453G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69966 AN: 151944 Hom.: 17830 Cov.: 31

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.461 AC: 70060 AN: 152062 Hom.: 17869 Cov.: 31 AF XY: 0.454 AC XY: 33716 AN XY: 74338

African (AFR) AF: 0.705 AC: 29229 AN: 41486

American (AMR) AF: 0.353 AC: 5388 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1585 AN: 5164

South Asian (SAS) AF: 0.451 AC: 2168 AN: 4810

European-Finnish (FIN) AF: 0.292 AC: 3093 AN: 10586

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.382 AC: 25988 AN: 67968

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.306 Hom.: 856

Bravo AF: 0.473

Asia WGS AF: 0.399 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.65
DANN	Benign	0.71
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs6925684; hg19: chr6-135936878;