15-77485290-C-T

Variant names:

• chr15-77485290-C-T
• rs7119
• NM_001304504.2:c.*2327C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 55 publications found

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]

ENSG00000279033 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HMG20A	NM_001304504.2	c.*2327C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000336216.9	NP_001291433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HMG20A	ENST00000336216.9	c.*2327C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_001304504.2	ENSP00000336856.4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.397 AC: 169 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AF: 0.750 AC: 3 AN: 4

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

African (AFR) AF: 0.467 AC: 19355 AN: 41460

American (AMR) AF: 0.367 AC: 5618 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3468

East Asian (EAS) AF: 0.169 AC: 876 AN: 5178

South Asian (SAS) AF: 0.306 AC: 1474 AN: 4822

European-Finnish (FIN) AF: 0.415 AC: 4381 AN: 10556

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29440 AN: 67964

Other (OTH) AF: 0.411 AC: 869 AN: 2116

Alfa AF: 0.421 Hom.: 34873

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
PhyloP100		0.013
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7119; hg19: chr15-77777632;