chr15-77454848-A-G

Variant names:

• chr15-77454848-A-G
• rs7178572
• NM_001304504.2:c.-4-3556A>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.-4-3556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 151,718 control chromosomes in the GnomAD database, including 30,377 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 0.63 (30377 hom., cov: 29)
• Consequence: HMG20A NM_001304504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 111 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]

ENSG00000294779 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304504.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMG20A	NM_001304504.2	MANE Select	c.-4-3556A>G		intron	N/A	NP_001291433.1	Q9NP66-1
	HMG20A	NM_018200.4		c.-4-3556A>G		intron	N/A	NP_060670.1	Q9NP66-1
	HMG20A	NM_001304505.2		c.-255-3556A>G		intron	N/A	NP_001291434.1	B4DMG1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HMG20A	ENST00000336216.9	TSL:1 MANE Select	c.-4-3556A>G		intron	N/A	ENSP00000336856.4	Q9NP66-1
	HMG20A	ENST00000381714.7	TSL:1	c.-4-3556A>G		intron	N/A	ENSP00000371133.3	Q9NP66-1
	HMG20A	ENST00000859564.1		c.-4-3556A>G		intron	N/A	ENSP00000529622.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94895 AN: 151600 Hom.: 30342 Cov.: 29

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.626 AC: 94986 AN: 151718 Hom.: 30377 Cov.: 29 AF XY: 0.618 AC XY: 45802 AN XY: 74126

African (AFR) AF: 0.526 AC: 21733 AN: 41338

American (AMR) AF: 0.612 AC: 9330 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2447 AN: 3462

East Asian (EAS) AF: 0.372 AC: 1912 AN: 5146

South Asian (SAS) AF: 0.500 AC: 2401 AN: 4800

European-Finnish (FIN) AF: 0.655 AC: 6883 AN: 10512

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48066 AN: 67906

Other (OTH) AF: 0.638 AC: 1348 AN: 2112

Alfa AF: 0.679 Hom.: 121912

Bravo AF: 0.623

Asia WGS AF: 0.501 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		0.16
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: rs7178572; hg19: chr15-77747190;