rs2208574

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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.668+38533G>A		intron	N/A
	AHI1-DT	ENST00000685995.1		n.782-22259G>A		intron	N/A
	AHI1-DT	ENST00000690403.2		n.508-55368G>A		intron	N/A

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

African (AFR) AF: 0.545 AC: 22566 AN: 41434

American (AMR) AF: 0.368 AC: 5631 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3464

East Asian (EAS) AF: 0.410 AC: 2120 AN: 5166

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4820

European-Finnish (FIN) AF: 0.227 AC: 2395 AN: 10562

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20237 AN: 67976

Other (OTH) AF: 0.370 AC: 776 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.48
PhyloP100		0.91

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2208574;

hg19: chr6-136075617;