rs2038549

Variant names:

• chr6-135731810-G-A
• rs2038549
• ENST00000655302.1:n.668+15864G>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+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

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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+15864G>A		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.781+42074G>A		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.1	n.507+42074G>A		intron_variant	Intron 4 of 5
AHI1-DT	ENST00000702072.1	n.481+42074G>A		intron_variant	Intron 4 of 7

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

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.268

Alfa AF: 0.275 Hom.: 762

Bravo AF: 0.268

Asia WGS AF: 0.400 AC: 1383 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038549; hg19: chr6-136052948;