chr20-2259995-T-G

Variant names:

• chr20-2259995-T-G
• rs6047696
• ENST00000651531.1:c.64+1930T>G

Variant summary

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

The ENST00000651531.1(ENSG00000286022):​c.64+1930T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.866 in 152,138 control chromosomes in the GnomAD database, including 57,204 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 0.87 (57204 hom., cov: 31)
• Consequence: ENSG00000286022 ENST00000651531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 2 publications found

Genes affected

ENSG00000286022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651531.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286022	ENST00000651531.1		c.64+1930T>G		intron	N/A	ENSP00000498584.1

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131649 AN: 152020 Hom.: 57147 Cov.: 31

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.866 AC: 131765 AN: 152138 Hom.: 57204 Cov.: 31 AF XY: 0.869 AC XY: 64595 AN XY: 74364

African (AFR) AF: 0.889 AC: 36861 AN: 41480

American (AMR) AF: 0.900 AC: 13758 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3042 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5161 AN: 5168

South Asian (SAS) AF: 0.919 AC: 4430 AN: 4822

European-Finnish (FIN) AF: 0.831 AC: 8804 AN: 10592

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.836 AC: 56863 AN: 68006

Other (OTH) AF: 0.862 AC: 1816 AN: 2106

Alfa AF: 0.848 Hom.: 38252

Bravo AF: 0.870

Asia WGS AF: 0.958 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs6047696; hg19: chr20-2240641;