rs6139516

Variant names:

• chr20-4668630-A-G
• rs6139516
• ENST00000652447.1:n.87+16432T>C

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.87+16432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,118 control chromosomes in the GnomAD database, including 6,523 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 0.27 (6523 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534
• Publications: 2 publications found

Genes affected

ENSG00000293214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652447.1. 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
	ENSG00000293214	ENST00000652447.1		n.87+16432T>C		intron	N/A
	ENSG00000293214	ENST00000773443.1		n.131+4934T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41581 AN: 152000 Hom.: 6509 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.274 AC: 41637 AN: 152118 Hom.: 6523 Cov.: 32 AF XY: 0.275 AC XY: 20453 AN XY: 74384

African (AFR) AF: 0.438 AC: 18157 AN: 41476

American (AMR) AF: 0.200 AC: 3061 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 789 AN: 3472

East Asian (EAS) AF: 0.270 AC: 1400 AN: 5188

South Asian (SAS) AF: 0.203 AC: 979 AN: 4830

European-Finnish (FIN) AF: 0.251 AC: 2657 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13860 AN: 67972

Other (OTH) AF: 0.261 AC: 551 AN: 2112

Alfa AF: 0.217 Hom.: 6325

Bravo AF: 0.278

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.81
PhyloP100		-0.53

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: rs6139516;

hg19: chr20-4649276;