rs10223338

Variant names:

• chr6-135680889-C-T
• rs10223338
• ENST00000421378.4:n.418+8460C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421378.4(AHI1-DT):​n.418+8460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 150,764 control chromosomes in the GnomAD database, including 5,515 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 (5515 hom., cov: 31)
• Consequence: AHI1-DT ENST00000421378.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.420+8460C>T		intron_variant	Intron 3 of 3
AHI1-DT	NR_152842.1	n.534+8460C>T		intron_variant	Intron 4 of 5
AHI1-DT	NR_152844.1	n.534+8460C>T		intron_variant	Intron 4 of 4
AHI1-DT	NR_152845.1	n.658+8460C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.418+8460C>T		intron_variant	Intron 3 of 3	1
AHI1-DT	ENST00000579944.1	n.116+8460C>T		intron_variant	Intron 1 of 2	2
AHI1-DT	ENST00000653664.1	n.558+8460C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38519 AN: 150700 Hom.: 5511 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.224

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.255 AC: 38517 AN: 150764 Hom.: 5515 Cov.: 31 AF XY: 0.253 AC XY: 18583 AN XY: 73594

African (AFR) AF: 0.124 AC: 5121 AN: 41346

American (AMR) AF: 0.314 AC: 4745 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 999 AN: 3462

East Asian (EAS) AF: 0.404 AC: 2074 AN: 5140

South Asian (SAS) AF: 0.360 AC: 1721 AN: 4778

European-Finnish (FIN) AF: 0.187 AC: 1867 AN: 9970

Middle Eastern (MID) AF: 0.220 AC: 63 AN: 286

European-Non Finnish (NFE) AF: 0.311 AC: 21054 AN: 67692

Other (OTH) AF: 0.260 AC: 539 AN: 2072

Alfa AF: 0.294 Hom.: 4546

Bravo AF: 0.257

Asia WGS AF: 0.344 AC: 1192 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.53
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10223338; hg19: chr6-136002027;