chr6-135615740-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_152842.1(AHI1-DT):​n.315-26453G>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 0.461 in 152,062 control chromosomes in the GnomAD database, including 17,869 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 0.46 ( 17869 hom., cov: 31)

Consequence

AHI1-DT
NR_152842.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.439
Variant links:
Genes affected
AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AHI1-DTNR_152842.1 linkuse as main transcriptn.315-26453G>A intron_variant, non_coding_transcript_variant
AHI1-DTNR_026805.1 linkuse as main transcriptn.201-26453G>A intron_variant, non_coding_transcript_variant
AHI1-DTNR_152844.1 linkuse as main transcriptn.315-26453G>A intron_variant, non_coding_transcript_variant
AHI1-DTNR_152845.1 linkuse as main transcriptn.439-26453G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AHI1-DTENST00000702072.1 linkuse as main transcriptn.148-26453G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.460
AC:
69966
AN:
151944
Hom.:
17830
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.704
Gnomad AMI
AF:
0.338
Gnomad AMR
AF:
0.353
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.307
Gnomad SAS
AF:
0.451
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.357
Gnomad NFE
AF:
0.382
Gnomad OTH
AF:
0.435
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.461
AC:
70060
AN:
152062
Hom.:
17869
Cov.:
31
AF XY:
0.454
AC XY:
33716
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.353
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.307
Gnomad4 SAS
AF:
0.451
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.382
Gnomad4 OTH
AF:
0.437
Alfa
AF:
0.280
Hom.:
666
Bravo
AF:
0.473
Asia WGS
AF:
0.399
AC:
1387
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.65
DANN
Benign
0.71

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6925684; hg19: chr6-135936878; API