rs6935033

chr6-135659499-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.399-12795G>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 0.51 in 152,056 control chromosomes in the GnomAD database, including 23,353 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 0.51 (23353 hom., cov: 32)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.399-12795G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.285-12795G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.399-12795G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.523-12795G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.232-12795G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77413 AN: 151938 Hom.: 23289 Cov.: 32

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.510 AC: 77533 AN: 152056 Hom.: 23353 Cov.: 32 AF XY: 0.503 AC XY: 37377 AN XY: 74316

Gnomad4 AFR AF: 0.853

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.497

Alfa AF: 0.427 Hom.: 3781

Bravo AF: 0.537

Asia WGS AF: 0.501 AC: 1740 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.13
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935033; hg19: chr6-135980637;