4-56703381-T-C

Variant names:

• chr4-56703381-T-C
• rs1824965
• ENST00000685954.2:n.565+190A>G

Variant summary

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

The ENST00000685954.2(CHAER1):​n.565+190A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 151,910 control chromosomes in the GnomAD database, including 19,056 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 0.50 (19056 hom., cov: 31)
• Consequence: CHAER1 ENST00000685954.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 3 publications found

Genes affected

CHAER1 (HGNC:53620): (cardiac hypertrophy associated epigenetic regulator 1)

ENSG00000310240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685954.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHAER1	ENST00000685954.2		n.565+190A>G		intron	N/A
	ENSG00000310240	ENST00000848501.1		n.137-434T>C		intron	N/A
	ENSG00000310240	ENST00000848502.1		n.255-434T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75249 AN: 151792 Hom.: 19054 Cov.: 31

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.495 AC: 75261 AN: 151910 Hom.: 19056 Cov.: 31 AF XY: 0.495 AC XY: 36740 AN XY: 74244

African (AFR) AF: 0.413 AC: 17114 AN: 41406

American (AMR) AF: 0.484 AC: 7373 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2095 AN: 3462

East Asian (EAS) AF: 0.398 AC: 2056 AN: 5166

South Asian (SAS) AF: 0.415 AC: 2003 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 5992 AN: 10540

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36969 AN: 67948

Other (OTH) AF: 0.494 AC: 1044 AN: 2114

Alfa AF: 0.516 Hom.: 45674

Bravo AF: 0.486

Asia WGS AF: 0.386 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.71
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs1824965; hg19: chr4-57569547;