ENST00000829139.1:n.227-15713A>G

Variant names:

• chr4-173680897-A-G
• rs11727767
• ENST00000829139.1:n.227-15713A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000829139.1(HAND2-AS1):​n.227-15713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,950 control chromosomes in the GnomAD database, including 20,844 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 0.52 (20844 hom., cov: 32)
• Consequence: HAND2-AS1 ENST00000829139.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAND2-AS1	ENST00000829139.1	n.227-15713A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79017 AN: 151832 Hom.: 20809 Cov.: 32

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.521 AC: 79105 AN: 151950 Hom.: 20844 Cov.: 32 AF XY: 0.521 AC XY: 38664 AN XY: 74242

African (AFR) AF: 0.587 AC: 24294 AN: 41422

American (AMR) AF: 0.560 AC: 8552 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1504 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1807 AN: 5172

South Asian (SAS) AF: 0.523 AC: 2508 AN: 4798

European-Finnish (FIN) AF: 0.484 AC: 5110 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33691 AN: 67948

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.501 Hom.: 58615

Bravo AF: 0.524

Asia WGS AF: 0.536 AC: 1865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.84
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11727767; hg19: chr4-174602048;