rs77067995

Variant names:

• chr20-62476223-G-A
• rs77067995
• NM_080473.5:c.-315C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080473.5(GATA5):​c.-315C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,248 control chromosomes in the GnomAD database, including 528 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 0.054 (528 hom., cov: 34)
• Consequence: GATA5 NM_080473.5 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

GATA5 (HGNC:15802): (GATA binding protein 5) The protein encoded by this gene is a transcription factor that contains two GATA-type zinc fingers. The encoded protein is known to bind to hepatocyte nuclear factor-1alpha (HNF-1alpha), and this interaction is essential for cooperative activation of the intestinal lactase-phlorizin hydrolase promoter. In other organisms, similar proteins may be involved in the establishment of cardiac smooth muscle cell diversity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA5	NM_080473.5	c.-315C>T		upstream_gene_variant		ENST00000252997.3	NP_536721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA5	ENST00000252997.3	c.-315C>T		upstream_gene_variant		1	NM_080473.5	ENSP00000252997.2

Frequencies

GnomAD3 genomes AF: 0.0539 AC: 8196 AN: 152130 Hom.: 524 Cov.: 34

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.0450

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.00198

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00863

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0540 AC: 8215 AN: 152248 Hom.: 528 Cov.: 34 AF XY: 0.0549 AC XY: 4091 AN XY: 74454

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.00951

Gnomad4 EAS AF: 0.0449

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.00198

Gnomad4 NFE AF: 0.00863

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0346 Hom.: 45

Bravo AF: 0.0563

Asia WGS AF: 0.111 AC: 385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77067995; hg19: chr20-61051279;