chr20-39229452-G-A

Variant names:

• chr20-39229452-G-A
• rs7271186
• ENST00000772859.1:n.458+9704G>A

Variant summary

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

The ENST00000772859.1(ENSG00000300599):​n.458+9704G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0604 in 152,244 control chromosomes in the GnomAD database, including 386 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 0.060 (386 hom., cov: 32)
• Consequence: ENSG00000300599 ENST00000772859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.191
• Publications: 3 publications found

Genes affected

ENSG00000300599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772859.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300599	ENST00000772859.1		n.458+9704G>A		intron	N/A
	ENSG00000300599	ENST00000772860.1		n.313+9704G>A		intron	N/A
	ENSG00000300599	ENST00000772861.1		n.313+9704G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0605 AC: 9197 AN: 152126 Hom.: 385 Cov.: 32

Gnomad AFR AF: 0.0251

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0570

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

GnomAD4 genome AF: 0.0604 AC: 9199 AN: 152244 Hom.: 386 Cov.: 32 AF XY: 0.0641 AC XY: 4770 AN XY: 74436

African (AFR) AF: 0.0250 AC: 1039 AN: 41542

American (AMR) AF: 0.0507 AC: 776 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3472

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5182

South Asian (SAS) AF: 0.213 AC: 1029 AN: 4822

European-Finnish (FIN) AF: 0.0695 AC: 736 AN: 10596

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4859 AN: 68022

Other (OTH) AF: 0.0565 AC: 119 AN: 2108

Alfa AF: 0.0683 Hom.: 686

Bravo AF: 0.0521

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.80
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs7271186; hg19: chr20-37858095;