rs9494335

Positions:

• chr6-135690726-A-G
• chr6-135690726-A-T

Variant summary

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

The ENST00000421378.4(AHI1-DT):​n.1522A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,048 control chromosomes in the GnomAD database, including 7,630 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 0.31 (7630 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AHI1-DT ENST00000421378.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

Genes affected

AHI1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.1524A>G		non_coding_transcript_exon_variant	4/4
AHI1-DT	NR_152844.1	n.1638A>G		non_coding_transcript_exon_variant	5/5
AHI1-DT	NR_152845.1	n.1762A>G		non_coding_transcript_exon_variant	5/5
AHI1-DT	NR_152842.1	n.648+990A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.1522A>G		non_coding_transcript_exon_variant	4/4	1
AHI1-DT	ENST00000653664.1	n.1662A>G		non_coding_transcript_exon_variant	5/5
AHI1-DT	ENST00000655480.1	n.1546A>G		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47632 AN: 151930 Hom.: 7619 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.316

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.313 AC: 47663 AN: 152048 Hom.: 7630 Cov.: 32 AF XY: 0.311 AC XY: 23083 AN XY: 74326

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.317

Alfa AF: 0.312 Hom.: 1328

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9494335; hg19: chr6-136011864;