15-77429767-A-G

Variant names:

• chr15-77429767-A-G
• rs10519165
• NM_001304504.2:c.-5+8763A>G

Variant summary

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

The NM_001304504.2(HMG20A):​c.-5+8763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 152,306 control chromosomes in the GnomAD database, including 563 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 0.077 (563 hom., cov: 32)
• Consequence: HMG20A NM_001304504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HMG20A	NM_001304504.2	c.-5+8763A>G		intron_variant	Intron 1 of 9	ENST00000336216.9	NP_001291433.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HMG20A	ENST00000336216.9	c.-5+8763A>G		intron_variant	Intron 1 of 9	1	NM_001304504.2	ENSP00000336856.4

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11714 AN: 152188 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0770 AC: 11726 AN: 152306 Hom.: 563 Cov.: 32 AF XY: 0.0767 AC XY: 5715 AN XY: 74468

African (AFR) AF: 0.0323 AC: 1342 AN: 41580

American (AMR) AF: 0.0988 AC: 1512 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.0208 AC: 108 AN: 5190

South Asian (SAS) AF: 0.0520 AC: 251 AN: 4830

European-Finnish (FIN) AF: 0.101 AC: 1068 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6973 AN: 68012

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0921 Hom.: 282

Bravo AF: 0.0752

Asia WGS AF: 0.0320 AC: 110 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.43
PhyloP100		0.41
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: rs10519165; hg19: chr15-77722109;