rs10223338

chr6-135680889-C-T

Variant summary

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

The NR_152842.1(AHI1-DT):n.534+8460C>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 0.255 in 150,764 control chromosomes in the GnomAD database, including 5,515 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 (5515 hom., cov: 31)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

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 = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.534+8460C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.420+8460C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.534+8460C>T		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.658+8460C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.367+8460C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38519 AN: 150700 Hom.: 5511 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.255 AC: 38517 AN: 150764 Hom.: 5515 Cov.: 31 AF XY: 0.253 AC XY: 18583 AN XY: 73594

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.289

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.260

Alfa AF: 0.295 Hom.: 3399

Bravo AF: 0.257

Asia WGS AF: 0.344 AC: 1192 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.17
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10223338; hg19: chr6-136002027;