6-135738039-G-T

Variant names:

• chr6-135738039-G-T
• rs2038551
• ENST00000655302.1:n.668+22093G>T

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+22093G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,108 control chromosomes in the GnomAD database, including 5,775 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 0.26 (5775 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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+22093G>T		intron	N/A
	AHI1-DT	ENST00000685995.1		n.782-38699G>T		intron	N/A
	AHI1-DT	ENST00000690403.2		n.507+48303G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39044 AN: 151988 Hom.: 5764 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.257 AC: 39072 AN: 152108 Hom.: 5775 Cov.: 32 AF XY: 0.254 AC XY: 18865 AN XY: 74366

African (AFR) AF: 0.129 AC: 5353 AN: 41510

American (AMR) AF: 0.324 AC: 4949 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1066 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2346 AN: 5174

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10578

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20668 AN: 67968

Other (OTH) AF: 0.264 AC: 559 AN: 2116

Alfa AF: 0.294 Hom.: 11524

Bravo AF: 0.262

Asia WGS AF: 0.397 AC: 1378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.71
DANN	Benign	0.74
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs2038551; hg19: chr6-136059177;