20-51943113-T-C

Variant names:

• chr20-51943113-T-C
• rs6068020
• ENST00000732944.1:n.91-29299A>G

Variant summary

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

The ENST00000732944.1(ENSG00000295844):​n.91-29299A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,022 control chromosomes in the GnomAD database, including 30,371 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 0.63 (30371 hom., cov: 33)
• Consequence: ENSG00000295844 ENST00000732944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 10 publications found

Genes affected

ENSG00000295844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 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
ENSG00000295844	ENST00000732944.1	n.91-29299A>G		intron_variant	Intron 1 of 4
ENSG00000295844	ENST00000732945.1	n.90-42876A>G		intron_variant	Intron 1 of 2
ENSG00000295844	ENST00000732946.1	n.286+18255A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95909 AN: 151904 Hom.: 30342 Cov.: 33

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.631 AC: 95977 AN: 152022 Hom.: 30371 Cov.: 33 AF XY: 0.631 AC XY: 46846 AN XY: 74296

African (AFR) AF: 0.615 AC: 25490 AN: 41470

American (AMR) AF: 0.665 AC: 10147 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2494 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2535 AN: 5166

South Asian (SAS) AF: 0.628 AC: 3022 AN: 4812

European-Finnish (FIN) AF: 0.629 AC: 6635 AN: 10556

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43388 AN: 67972

Other (OTH) AF: 0.655 AC: 1385 AN: 2114

Alfa AF: 0.641 Hom.: 144886

Bravo AF: 0.635

Asia WGS AF: 0.573 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.83
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6068020; hg19: chr20-50559652;