6-135698009-C-T

Position:

• chr6-135698009-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579944.1(AHI1-DT):​n.230+8273C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,076 control chromosomes in the GnomAD database, including 5,841 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 (5841 hom., cov: 32)
• Consequence: AHI1-DT ENST00000579944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

AHI1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_152842.1	n.648+8273C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000579944.1	n.230+8273C>T		intron_variant		2
AHI1-DT	ENST00000655302.1	n.543+8273C>T		intron_variant
AHI1-DT	ENST00000685995.1	n.781+8273C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39732 AN: 151958 Hom.: 5832 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.261 AC: 39751 AN: 152076 Hom.: 5841 Cov.: 32 AF XY: 0.259 AC XY: 19266 AN XY: 74320

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.259

Alfa AF: 0.304 Hom.: 9647

Bravo AF: 0.260

Asia WGS AF: 0.354 AC: 1228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12202212; hg19: chr6-136019147;