15-77485290-C-T

Position:

• chr15-77485290-C-T

Variant summary

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

The NM_001304504.2(HMG20A):​c.*2327C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,494 control chromosomes in the GnomAD database, including 13,643 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 0.42 (13606 hom., cov: 32)
  • Exomes 𝑓: 0.41 (37 hom.)
• Consequence: HMG20A NM_001304504.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

HMG20A (HGNC:5001): (high mobility group 20A) Enables identical protein binding activity. Predicted to be involved in regulation of gene expression. Predicted to act upstream of or within negative regulation of neuron differentiation; negative regulation of protein sumoylation; and negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HMG20A	NM_001304504.2	c.*2327C>T		3_prime_UTR_variant	10/10	ENST00000336216.9	NP_001291433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HMG20A	ENST00000336216.9	c.*2327C>T		3_prime_UTR_variant	10/10	1	NM_001304504.2	ENSP00000336856	P1
HMG20A	ENST00000381714.7	c.*2327C>T		3_prime_UTR_variant	11/11	1		ENSP00000371133	P1
	ENST00000623172.1	n.317G>A		non_coding_transcript_exon_variant	1/1
HMG20A	ENST00000558288.1	n.3241C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63840 AN: 151940 Hom.: 13574 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.404

GnomAD4 exome AF: 0.406 AC: 177 AN: 436 Hom.: 37 Cov.: 0 AF XY: 0.366 AC XY: 96 AN XY: 262

Gnomad4 FIN exome AF: 0.397

Gnomad4 NFE exome AF: 0.833

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.420 AC: 63933 AN: 152058 Hom.: 13606 Cov.: 32 AF XY: 0.414 AC XY: 30771 AN XY: 74344

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.411

Alfa AF: 0.419 Hom.: 21313

Bravo AF: 0.420

Asia WGS AF: 0.314 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.27

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

Other links and lift over

dbSNP: rs7119; hg19: chr15-77777632;