rs947583

Variant names:

• chr6-135812521-T-C
• rs947583
• ENST00000655302.1:n.2747T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655302.1(AHI1-DT):​n.2747T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 152,180 control chromosomes in the GnomAD database, including 5,785 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 0.27 (5785 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 23 publications found

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655302.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AHI1-DT	ENST00000655302.1		n.2747T>C		non_coding_transcript_exon	Exon 7 of 7
	AHI1-DT	ENST00000702072.1		n.809+1751T>C		intron	N/A
	AHI1-DT	ENST00000808297.1		n.502+1751T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41376 AN: 152062 Hom.: 5771 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.272 AC: 41411 AN: 152180 Hom.: 5785 Cov.: 32 AF XY: 0.267 AC XY: 19884 AN XY: 74374

African (AFR) AF: 0.265 AC: 11015 AN: 41518

American (AMR) AF: 0.298 AC: 4560 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3468

East Asian (EAS) AF: 0.356 AC: 1837 AN: 5162

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4822

European-Finnish (FIN) AF: 0.140 AC: 1480 AN: 10594

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18781 AN: 68002

Other (OTH) AF: 0.272 AC: 576 AN: 2116

Alfa AF: 0.281 Hom.: 25753

Bravo AF: 0.280

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.0
DANN	Benign	0.68
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs947583; hg19: chr6-136133659;