6-135738285-A-G

Variant names:

• chr6-135738285-A-G
• rs911507
• ENST00000655302.1:n.668+22339A>G

Variant summary

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

The ENST00000655302.1(AHI1-DT):​n.668+22339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,038 control chromosomes in the GnomAD database, including 21,643 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 0.48 (21643 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655302.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000655302.1		n.668+22339A>G		intron	N/A
	AHI1-DT	ENST00000685995.1		n.782-38453A>G		intron	N/A
	AHI1-DT	ENST00000690403.2		n.507+48549A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73224 AN: 151920 Hom.: 21577 Cov.: 32

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.482 AC: 73348 AN: 152038 Hom.: 21643 Cov.: 32 AF XY: 0.474 AC XY: 35204 AN XY: 74310

African (AFR) AF: 0.831 AC: 34481 AN: 41470

American (AMR) AF: 0.438 AC: 6677 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2351 AN: 5162

South Asian (SAS) AF: 0.519 AC: 2498 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1821 AN: 10590

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.333 AC: 22624 AN: 67962

Other (OTH) AF: 0.472 AC: 998 AN: 2116

Alfa AF: 0.391 Hom.: 16632

Bravo AF: 0.515

Asia WGS AF: 0.491 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs911507; hg19: chr6-136059423;