20-5714407-T-C

Variant names:

• chr20-5714407-T-C
• rs6085252
• ENST00000720651.1:n.73+914A>G

Variant summary

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

The ENST00000720651.1(ENSG00000294032):​n.73+914A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,174 control chromosomes in the GnomAD database, including 2,840 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 0.19 (2840 hom., cov: 30)
• Consequence: ENSG00000294032 ENST00000720651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 4 publications found

Genes affected

ENSG00000294032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720651.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294032	ENST00000720651.1		n.73+914A>G		intron	N/A
	ENSG00000294032	ENST00000720652.1		n.126+150A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28536 AN: 152056 Hom.: 2835 Cov.: 30

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.188 AC: 28580 AN: 152174 Hom.: 2840 Cov.: 30 AF XY: 0.187 AC XY: 13911 AN XY: 74376

African (AFR) AF: 0.245 AC: 10182 AN: 41514

American (AMR) AF: 0.190 AC: 2905 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.180 AC: 933 AN: 5176

South Asian (SAS) AF: 0.193 AC: 928 AN: 4820

European-Finnish (FIN) AF: 0.113 AC: 1196 AN: 10600

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.163 AC: 11083 AN: 68000

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.176 Hom.: 4560

Bravo AF: 0.197

Asia WGS AF: 0.179 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.5
DANN	Benign	0.89
PhyloP100		-0.028

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6085252;

hg19: chr20-5695053;