rs6139516

Positions:

• chr20-4668630-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652447.1(ENSG00000293214):​n.87+16432T>C variant causes a intron, non coding transcript 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: ENST00000652447.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.534

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652447.1	n.87+16432T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.261

Alfa AF: 0.210 Hom.: 4549

Bravo AF: 0.278

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6139516; hg19: chr20-4649276;