rs878854746

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004821.3(HAND1):​c.289G>T​(p.Gly97Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

HAND1
NM_004821.3 missense

Scores

2
11
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.62
Variant links:
Genes affected
HAND1 (HGNC:4807): (heart and neural crest derivatives expressed 1) The protein encoded by this gene belongs to the basic helix-loop-helix family of transcription factors. This gene product is one of two closely related family members, the HAND proteins, which are asymmetrically expressed in the developing ventricular chambers and play an essential role in cardiac morphogenesis. Working in a complementary fashion, they function in the formation of the right ventricle and aortic arch arteries, implicating them as mediators of congenital heart disease. In addition, it has been suggested that this transcription factor may be required for early trophoblast differentiation. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HAND1NM_004821.3 linkc.289G>T p.Gly97Cys missense_variant 1/2 ENST00000231121.3 NP_004812.1
HAND1XM_005268531.2 linkc.289G>T p.Gly97Cys missense_variant 1/2 XP_005268588.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HAND1ENST00000231121.3 linkc.289G>T p.Gly97Cys missense_variant 1/21 NM_004821.3 ENSP00000231121.2 O96004

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Hypoplastic left heart syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 01, 2016Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, this is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a HAND1-related disease. This sequence change replaces glycine with cysteine at codon 97 of the HAND1 protein (p.Gly97Cys). The glycine residue is highly conserved and there is a large physicochemical difference between glycine and cysteine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
-0.040
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.85
D
Eigen
Benign
-0.17
Eigen_PC
Benign
-0.086
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Benign
0.74
T
M_CAP
Pathogenic
0.31
D
MetaRNN
Uncertain
0.55
D
MetaSVM
Uncertain
0.32
D
MutationAssessor
Benign
0.26
N
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-3.4
D
REVEL
Uncertain
0.50
Sift
Uncertain
0.013
D
Sift4G
Uncertain
0.020
D
Polyphen
0.83
P
Vest4
0.48
MutPred
0.41
Gain of methylation at K96 (P = 0.0139);
MVP
0.99
MPC
1.4
ClinPred
0.88
D
GERP RS
3.2
Varity_R
0.36
gMVP
0.47

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs878854746; hg19: chr5-153857280; API