20-24934659-A-G

Variant names:

• chr20-24934659-A-G
• rs6050164
• ENST00000776975.1:n.75+15782T>C

Variant summary

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

The ENST00000776975.1(ENSG00000301203):​n.75+15782T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0899 in 152,302 control chromosomes in the GnomAD database, including 698 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 0.090 (698 hom., cov: 33)
• Consequence: ENSG00000301203 ENST00000776975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 publications found

Genes affected

ENSG00000301203 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0998 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776975.1. 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
	ENSG00000301203	ENST00000776975.1		n.75+15782T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0899 AC: 13676 AN: 152182 Hom.: 698 Cov.: 33

Gnomad AFR AF: 0.0993

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0788

Gnomad ASJ AF: 0.0614

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0417

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0918

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

GnomAD4 genome AF: 0.0899 AC: 13693 AN: 152302 Hom.: 698 Cov.: 33 AF XY: 0.0864 AC XY: 6434 AN XY: 74490

African (AFR) AF: 0.0995 AC: 4133 AN: 41556

American (AMR) AF: 0.0786 AC: 1203 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.0614 AC: 213 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5184

South Asian (SAS) AF: 0.0967 AC: 467 AN: 4828

European-Finnish (FIN) AF: 0.0417 AC: 443 AN: 10630

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.102 AC: 6923 AN: 68002

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.0893 Hom.: 117

Bravo AF: 0.0920

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.92
DANN	Benign	0.63
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6050164; hg19: chr20-24915295;