Genetic Variant AHI1-DT:n.199-5539A>T (chr6-135636654-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000421378.4(AHI1-DT):n.199-5539A>T variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AHI1-DT
ENST00000421378.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.25

Publications

2 publications found

Variant links:

Genes affected

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

AHI1-DT links:

HMGB1P17 (HGNC:39099): (high mobility group box 1 pseudogene 17)

HMGB1P17 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
HMGB1P17		n.135636654A>T	intragenic_variant
AHI1-DT	NR_026805.1 link	n.201-5539A>T	intron_variant	Intron 1 of 3
AHI1-DT	NR_152842.1 link	n.315-5539A>T	intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AHI1-DT	ENST00000421378.4 link	n.199-5539A>T	intron_variant	Intron 1 of 3	1
HMGB1P17	ENST00000403495.2 link	n.60T>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
AHI1-DT	ENST00000438618.2 link	n.439+803A>T	intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

17648

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

10788

African (AFR)

AF:

0.00

AC:

AN:

590

American (AMR)

AF:

0.00

AC:

AN:

2356

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

324

East Asian (EAS)

AF:

0.00

AC:

AN:

1060

South Asian (SAS)

AF:

0.00

AC:

AN:

1888

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1692

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

9024

Other (OTH)

AF:

0.00

AC:

AN:

692

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

6154

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.8

(source)

DANN

Benign

0.40

PhyloP100

4.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over