rs1475069

Variant names:

• chr6-135735096-A-C
• rs1475069
• ENST00000655302.1:n.668+19150A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-135735096-A-C
• chr6-135735096-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000655302.1(AHI1-DT):​n.668+19150A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,186 control chromosomes in the GnomAD database, including 5,578 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 0.25 (5578 hom., cov: 32)
• Consequence: AHI1-DT ENST00000655302.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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+19150A>C		intron_variant	Intron 5 of 6
AHI1-DT	ENST00000685995.1	n.782-41642A>C		intron_variant	Intron 5 of 7
AHI1-DT	ENST00000690403.2	n.507+45360A>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37371 AN: 152066 Hom.: 5569 Cov.: 32

Gnomad AFR AF: 0.0898

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.246 AC: 37387 AN: 152186 Hom.: 5578 Cov.: 32 AF XY: 0.243 AC XY: 18106 AN XY: 74406

African (AFR) AF: 0.0897 AC: 3727 AN: 41550

American (AMR) AF: 0.321 AC: 4905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2341 AN: 5168

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

European-Finnish (FIN) AF: 0.162 AC: 1711 AN: 10594

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

European-Non Finnish (NFE) AF: 0.304 AC: 20679 AN: 67988

Other (OTH) AF: 0.256 AC: 541 AN: 2112

Alfa AF: 0.279 Hom.: 8118

Bravo AF: 0.249

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		0.093

Splicing

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

Other links and lift over

dbSNP: rs1475069; hg19: chr6-136056234; COSMIC: COSV69427648;