6-135519918-C-A

Position:

• chr6-135519918-C-A

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+21401C>A 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 0.699 in 151,886 control chromosomes in the GnomAD database, including 37,601 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 0.70 (37601 hom., cov: 30)
• Consequence: AHI1-DT NR_152842.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_152842.1	n.314+21401C>A		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+21918C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106127 AN: 151768 Hom.: 37556 Cov.: 30

Gnomad AFR AF: 0.821

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.699 AC: 106226 AN: 151886 Hom.: 37601 Cov.: 30 AF XY: 0.701 AC XY: 51990 AN XY: 74210

Gnomad4 AFR AF: 0.821

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.683

Alfa AF: 0.693 Hom.: 5234

Bravo AF: 0.706

Asia WGS AF: 0.678 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.080
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9647635; hg19: chr6-135841056; COSMIC: COSV69848620;