rs2208574

Variant names:

• chr6-135754479-G-A
• rs2208574
• ENST00000655302.1:n.668+38533G>A

Variant summary

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

The ENST00000655302.1(AHI1-DT):​n.668+38533G>A variant causes a intron 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 ENST00000655302.1 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000655302.1	n.668+38533G>A		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.782-22259G>A		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.1	n.508-55368G>A		intron_variant	Intron 4 of 5
AHI1-DT	ENST00000702072.1	n.482-55368G>A		intron_variant	Intron 4 of 7

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;