6-135689660-A-C

Position:

• chr6-135689660-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000421378.4(AHI1-DT):​n.456A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00822 in 151,876 control chromosomes in the GnomAD database, including 15 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 0.0082 (15 hom., cov: 32)
  • Exomes 𝑓: 0.015 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: AHI1-DT ENST00000421378.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.91).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00822 (1248/151876) while in subpopulation SAS AF= 0.0415 (200/4814). AF 95% confidence interval is 0.0368. There are 15 homozygotes in gnomad4. There are 652 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 15 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AHI1-DT	NR_026805.1	n.458A>C		non_coding_transcript_exon_variant	4/4
AHI1-DT	NR_152842.1	n.572A>C		non_coding_transcript_exon_variant	5/6
AHI1-DT	NR_152844.1	n.572A>C		non_coding_transcript_exon_variant	5/5
AHI1-DT	NR_152845.1	n.696A>C		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AHI1-DT	ENST00000421378.4	n.456A>C		non_coding_transcript_exon_variant	4/4	1
AHI1-DT	ENST00000579944.1	n.154A>C		non_coding_transcript_exon_variant	2/3	2
AHI1-DT	ENST00000653664.1	n.596A>C		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.00822 AC: 1248 AN: 151758 Hom.: 15 Cov.: 32

Gnomad AFR AF: 0.00174

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00643

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.0415

Gnomad FIN AF: 0.00730

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.00670

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0147 AC: 1 AN: 68 Hom.: 0 Cov.: 0 AF XY: 0.0227 AC XY: 1 AN XY: 44

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0185

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00822 AC: 1248 AN: 151876 Hom.: 15 Cov.: 32 AF XY: 0.00879 AC XY: 652 AN XY: 74206

Gnomad4 AFR AF: 0.00174

Gnomad4 AMR AF: 0.00643

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.00213

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.00730

Gnomad4 NFE AF: 0.0104

Gnomad4 OTH AF: 0.00663

Alfa AF: 0.00189 Hom.: 295

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	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2273069; hg19: chr6-136010798;