rs2208574

chr6-135754479-G-A

Variant summary

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

The ENST00000702072.1(AHI1-DT):n.482-55368G>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 0.376 in 152,022 control chromosomes in the GnomAD database, including 11,722 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 0.38 (11722 hom., cov: 32)
• Consequence: AHI1-DT ENST00000702072.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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.482-55368G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000655302.1	n.668+38533G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000685995.1	n.782-22259G>A		intron_variant, non_coding_transcript_variant
AHI1-DT	ENST00000690403.1	n.508-55368G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57058 AN: 151904 Hom.: 11680 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.376 AC: 57150 AN: 152022 Hom.: 11722 Cov.: 32 AF XY: 0.372 AC XY: 27600 AN XY: 74292

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.370

Alfa AF: 0.342 Hom.: 1611

Bravo AF: 0.392

Asia WGS AF: 0.375 AC: 1304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.9
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2208574; hg19: chr6-136075617;