chr20-4631231-G-A

Variant names:

• chr20-4631231-G-A
• rs6052699
• ENST00000652447.1:n.88-1010C>T

Variant summary

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

The ENST00000652447.1(ENSG00000293214):​n.88-1010C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,990 control chromosomes in the GnomAD database, including 27,667 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 0.59 (27667 hom., cov: 32)
• Consequence: ENSG00000293214 ENST00000652447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.962
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293214	ENST00000652447.1	n.88-1010C>T		intron_variant	Intron 1 of 1
ENSG00000293214	ENST00000773443.1	n.132-1010C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89864 AN: 151874 Hom.: 27622 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.592 AC: 89963 AN: 151990 Hom.: 27667 Cov.: 32 AF XY: 0.591 AC XY: 43881 AN XY: 74274

African (AFR) AF: 0.764 AC: 31665 AN: 41456

American (AMR) AF: 0.595 AC: 9085 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3468

East Asian (EAS) AF: 0.517 AC: 2675 AN: 5176

South Asian (SAS) AF: 0.504 AC: 2420 AN: 4800

European-Finnish (FIN) AF: 0.572 AC: 6024 AN: 10524

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34459 AN: 67974

Other (OTH) AF: 0.541 AC: 1143 AN: 2112

Alfa AF: 0.531 Hom.: 99462

Bravo AF: 0.598

Asia WGS AF: 0.587 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.8
DANN	Benign	0.41
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs6052699; hg19: chr20-4611877;