Variant rs11944332 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000647106.1(HAND2-AS1):n.142-930A>G 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 0.117 in 787,432 control chromosomes in the GnomAD database, including 6,122 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 0.11 ( 1042 hom., cov: 32)

Exomes 𝑓: 0.12 ( 5080 hom. )

Consequence

HAND2-AS1
ENST00000647106.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.85

Variant links:

Genes affected

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:

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

RANP6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAND2-AS1	ENST00000647106.1 linkuse as main transcript	n.142-930A>G		intron_variant, non_coding_transcript_variant
RANP6	ENST00000413691.2 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17243

AN:

152086

Hom.:

1041

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.127

Gnomad AMR

AF:

0.0823

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.00675

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.113

GnomAD4 exome

AF:

0.118

AC:

75108

AN:

635228

Hom.:

5080

Cov.:

AF XY:

0.119

AC XY:

40536

AN XY:

339322

show subpopulations

Gnomad4 AFR exome

AF:

0.101

Gnomad4 AMR exome

AF:

0.0650

Gnomad4 ASJ exome

AF:

0.125

Gnomad4 EAS exome

AF:

0.00565

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.107

Gnomad4 NFE exome

AF:

0.132

Gnomad4 OTH exome

AF:

0.119

GnomAD4 genome

AF:

0.113

AC:

17253

AN:

152204

Hom.:

1042

Cov.:

AF XY:

0.109

AC XY:

8148

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.0822

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.00676

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.108

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.122

Hom.:

130

Bravo

AF:

0.111

Asia WGS

AF:

0.0680

AC:

237

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

7.2

DANN

Benign

0.67

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over