Genetic Variant IQCH-AS1:n.429+1348C>T (chr15-67517652-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000561232.5(IQCH-AS1):n.429+1348C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00542 in 152,278 control chromosomes in the GnomAD database, including 6 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 0.0054 ( 6 hom., cov: 32)

Consequence

IQCH-AS1
ENST00000561232.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.607

Publications

1 publications found

Variant links:

Genes affected

IQCH-AS1 (HGNC:44104): (IQCH antisense RNA 1)

IQCH-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
IQCH-AS1	NR_040051.1 link	n.402+1348C>T	intron_variant	Intron 2 of 5
IQCH-AS1	NR_040052.1 link	n.429+1348C>T	intron_variant	Intron 2 of 5
IQCH-AS1	NR_040054.1 link	n.454+1348C>T	intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
IQCH-AS1	ENST00000561232.5 link	n.429+1348C>T	intron_variant	Intron 2 of 5	1
IQCH-AS1	ENST00000559285.1 link	n.274+1348C>T	intron_variant	Intron 2 of 4	2
IQCH-AS1	ENST00000559298.5 link	n.91+3894C>T	intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.00543

AC:

826

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00295

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00113

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00986

Gnomad OTH

AF:

0.00431

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

GnomAD4 genome

AF:

0.00542

AC:

825

AN:

152278

Hom.:

Cov.:

AF XY:

0.00465

AC XY:

346

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.00176

AC:

AN:

41556

American (AMR)

AF:

0.00294

AC:

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00230

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00113

AC:

AN:

10584

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00986

AC:

671

AN:

68030

Other (OTH)

AF:

0.00426

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

136

181

226

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00598

Hom.:

Bravo

AF:

0.00540

Asia WGS

AF:

0.000867

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.67

(source)

DANN

Benign

0.51

PhyloP100

-0.61

Splicing

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

Publications

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15-67517652-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over