rs12203875

chr6-135539276-G-Achr6-135539276-G-C

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+40759G>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 0.44 in 151,924 control chromosomes in the GnomAD database, including 17,760 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 0.44 (17760 hom., cov: 31)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.314+40759G>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+41276G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66881 AN: 151806 Hom.: 17762 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.440 AC: 66879 AN: 151924 Hom.: 17760 Cov.: 31 AF XY: 0.450 AC XY: 33396 AN XY: 74242

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.444

Alfa AF: 0.465 Hom.: 3766

Bravo AF: 0.418

Asia WGS AF: 0.505 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.66
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12203875; hg19: chr6-135860414;