6-135605725-A-G

Position:

• chr6-135605725-A-G

Variant summary

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

The NR_152842.1(AHI1-DT):​n.315-36468A>G variant causes a intron, non coding transcript 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 NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.315-36468A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.201-36468A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.315-36468A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.439-36468A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.148-36468A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.487

Alfa AF: 0.413 Hom.: 13906

Bravo AF: 0.510

Asia WGS AF: 0.419 AC: 1455 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896156; hg19: chr6-135926863;