rs3783457

Variant names:

• chr1-67684990-C-A
• rs3783457
• NM_001924.4:c.-505C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-67684990-C-A
• chr1-67684990-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001924.4(GADD45A):​c.-505C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 158,328 control chromosomes in the GnomAD database, including 37 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 0.012 (37 hom., cov: 33)
  • Exomes 𝑓: 0.00033 (0 hom.)
• Consequence: GADD45A NM_001924.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

Genes affected

GADD45A (HGNC:4095): (growth arrest and DNA damage inducible alpha) This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The protein encoded by this gene responds to environmental stresses by mediating activation of the p38/JNK pathway via MTK1/MEKK4 kinase. The DNA damage-induced transcription of this gene is mediated by both p53-dependent and -independent mechanisms. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.[provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0123 (1878/152292) while in subpopulation AFR AF= 0.0426 (1772/41566). AF 95% confidence interval is 0.041. There are 37 homozygotes in gnomad4. There are 905 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1878 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GADD45A	NM_001924.4	c.-505C>A		upstream_gene_variant		ENST00000370986.9	NP_001915.1
GADD45A	NM_001199741.2	c.-505C>A		upstream_gene_variant			NP_001186670.1
GADD45A	NM_001199742.2	c.-505C>A		upstream_gene_variant			NP_001186671.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GADD45A	ENST00000370986.9	c.-505C>A		upstream_gene_variant		1	NM_001924.4	ENSP00000360025.4

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1871 AN: 152174 Hom.: 37 Cov.: 33

Gnomad AFR AF: 0.0426

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00451

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000176

Gnomad OTH AF: 0.00716

GnomAD4 exome AF: 0.000331 AC: 2 AN: 6036 Hom.: 0 AF XY: 0.000304 AC XY: 1 AN XY: 3294

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0208

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00275

GnomAD4 genome AF: 0.0123 AC: 1878 AN: 152292 Hom.: 37 Cov.: 33 AF XY: 0.0122 AC XY: 905 AN XY: 74456

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.00451

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000176

Gnomad4 OTH AF: 0.00709

Alfa AF: 0.00610 Hom.: 1

Bravo AF: 0.0138

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3783457; hg19: chr1-68150673;