rs2143681

chr6-135611867-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.315-30326G>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 0.461 in 152,004 control chromosomes in the GnomAD database, including 17,856 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 0.46 (17856 hom., cov: 32)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.315-30326G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.201-30326G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.315-30326G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.439-30326G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.148-30326G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69949 AN: 151888 Hom.: 17818 Cov.: 32

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.461 AC: 70041 AN: 152004 Hom.: 17856 Cov.: 32 AF XY: 0.454 AC XY: 33707 AN XY: 74304

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.437

Alfa AF: 0.388 Hom.: 19601

Bravo AF: 0.473

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	-0.92
Cadd	Benign	0.83
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143681; hg19: chr6-135933005;