6-135530435-G-A

Position:

• chr6-135530435-G-A

Variant summary

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

The NR_152842.1(AHI1-DT):​n.314+31918G>A 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 0.257 in 152,068 control chromosomes in the GnomAD database, including 10,614 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 0.26 (10614 hom., cov: 32)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.314+31918G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.147+32435G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39012 AN: 151950 Hom.: 10578 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0598

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0860

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0873

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.257 AC: 39109 AN: 152068 Hom.: 10614 Cov.: 32 AF XY: 0.249 AC XY: 18488 AN XY: 74364

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0598

Gnomad4 EAS AF: 0.0961

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.0442

Gnomad4 NFE AF: 0.0873

Gnomad4 OTH AF: 0.236

Alfa AF: 0.105 Hom.: 3322

Bravo AF: 0.285

Asia WGS AF: 0.171 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494266; hg19: chr6-135851573;