6-135508658-T-C

Position:

• chr6-135508658-T-C

Variant summary

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

The NR_152842.1(AHI1-DT):​n.314+10141T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.863 in 152,230 control chromosomes in the GnomAD database, including 57,695 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 0.86 (57695 hom., cov: 32)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.57

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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_152842.1	n.314+10141T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000702072.1	n.147+10658T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131293 AN: 152112 Hom.: 57673 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.863 AC: 131372 AN: 152230 Hom.: 57695 Cov.: 32 AF XY: 0.868 AC XY: 64598 AN XY: 74434

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.957

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.976

Gnomad4 NFE AF: 0.932

Gnomad4 OTH AF: 0.867

Alfa AF: 0.922 Hom.: 87803

Bravo AF: 0.850

Asia WGS AF: 0.911 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4896151; hg19: chr6-135829796;