rs9399158

chr6-135727672-C-T

Variant summary

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

The ENST00000702072.1(AHI1-DT):n.481+37936C>T 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 0.262 in 152,008 control chromosomes in the GnomAD database, including 5,871 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 (5871 hom., cov: 32)
• Consequence: AHI1-DT ENST00000702072.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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 (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.481+37936C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000655302.1	n.668+11726C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000685995.1	n.781+37936C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000690403.1	n.507+37936C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39737 AN: 151890 Hom.: 5857 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.262 AC: 39778 AN: 152008 Hom.: 5871 Cov.: 32 AF XY: 0.259 AC XY: 19220 AN XY: 74278

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.268

Alfa AF: 0.275 Hom.: 762

Bravo AF: 0.268

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.15
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9399158; hg19: chr6-136048810; COSMIC: COSV70782686;