chr6-135731810-G-A

Variant names:

• chr6-135731810-G-A
• rs2038549
• ENST00000655302.1:n.668+15864G>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+15864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 151,948 control chromosomes in the GnomAD database, including 5,884 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 (5884 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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+15864G>A		intron	N/A
	AHI1-DT	ENST00000685995.1		n.781+42074G>A		intron	N/A
	AHI1-DT	ENST00000690403.2		n.507+42074G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39792 AN: 151828 Hom.: 5870 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.262 AC: 39832 AN: 151948 Hom.: 5884 Cov.: 32 AF XY: 0.259 AC XY: 19263 AN XY: 74260

African (AFR) AF: 0.146 AC: 6045 AN: 41446

American (AMR) AF: 0.326 AC: 4973 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2365 AN: 5170

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1710 AN: 10520

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20687 AN: 67952

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.269 Hom.: 767

Bravo AF: 0.268

Asia WGS AF: 0.400 AC: 1383 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2038549; hg19: chr6-136052948;