chr6-135506535-A-G

Variant names:

• chr6-135506535-A-G
• rs7750586
• ENST00000421378.4:n.198+8535A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421378.4(AHI1-DT):​n.198+8535A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,066 control chromosomes in the GnomAD database, including 7,337 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 0.30 (7337 hom., cov: 32)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.200+8535A>G		intron_variant	Intron 1 of 3
AHI1-DT	NR_152842.1	n.314+8018A>G		intron_variant	Intron 2 of 5
AHI1-DT	NR_152843.1	n.314+8018A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.198+8535A>G		intron_variant	Intron 1 of 3	1
AHI1-DT	ENST00000579339.6	n.156+8018A>G		intron_variant	Intron 2 of 3	1
AHI1-DT	ENST00000580741.5	n.399+7094A>G		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45674 AN: 151948 Hom.: 7332 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.300 AC: 45692 AN: 152066 Hom.: 7337 Cov.: 32 AF XY: 0.299 AC XY: 22229 AN XY: 74340

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.317

Alfa AF: 0.318 Hom.: 1809

Bravo AF: 0.294

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7750586; hg19: chr6-135827673;