Genetic Variant RANP6:n.173633681A>C (chr4-173633681-A-C) – 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 variant allele was found at a frequency of 0.00000157 in 635,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 0.0000016 ( 0 hom. )

Consequence

RANP6
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Publications

0 publications found

Variant links:

Genes affected

RANP6 (HGNC:39861): (RAN pseudogene 6)

RANP6 links:

HAND2-AS1 (HGNC:48872): (HAND2 antisense RNA 1) Predicted to be involved in positive regulation of gene expression. Predicted to act upstream of or within with a positive effect on cardiac right ventricle morphogenesis. Predicted to act upstream of or within transcription elongation from RNA polymerase II promoter. Predicted to be located in chromatin; cytoplasm; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

HAND2-AS1 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=-0.6).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647106.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
HAND2-AS1	ENST00000647106.1	n.142-930A>C	intron	N/A
HAND2-AS1	ENST00000829139.1	n.226+24470A>C	intron	N/A
HAND2-AS1	ENST00000829140.1	n.388-930A>C	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000157

AC:

AN:

635892

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

339698

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

16930

American (AMR)

AF:

0.00

AC:

AN:

33574

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16420

East Asian (EAS)

AF:

0.00

AC:

AN:

33118

South Asian (SAS)

AF:

0.00

AC:

AN:

60254

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42320

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2888

European-Non Finnish (NFE)

AF:

0.00000251

AC:

AN:

399014

Other (OTH)

AF:

0.00

AC:

AN:

31374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

6.9

(source)

DANN

Benign

0.68

PhyloP100

1.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over