chr20-2256129-G-A

Variant names:

• chr20-2256129-G-A
• rs6082527
• ENST00000651531.1:c.-48-1825G>A

Variant summary

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

The ENST00000651531.1(ENSG00000286022):​c.-48-1825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 152,288 control chromosomes in the GnomAD database, including 59,696 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 0.88 (59696 hom., cov: 34)
• Consequence: ENSG00000286022 ENST00000651531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 4 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=-0.91).
• 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

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
	ENSG00000286022	ENST00000651531.1		c.-48-1825G>A		intron	N/A	ENSP00000498584.1	A0A494C0J7

Frequencies

GnomAD3 genomes AF: 0.883 AC: 134355 AN: 152170 Hom.: 59636 Cov.: 34

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.913

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.883 AC: 134474 AN: 152288 Hom.: 59696 Cov.: 34 AF XY: 0.883 AC XY: 65731 AN XY: 74458

African (AFR) AF: 0.961 AC: 39969 AN: 41570

American (AMR) AF: 0.903 AC: 13827 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3116 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5167 AN: 5174

South Asian (SAS) AF: 0.913 AC: 4410 AN: 4828

European-Finnish (FIN) AF: 0.798 AC: 8466 AN: 10608

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.833 AC: 56619 AN: 68004

Other (OTH) AF: 0.876 AC: 1853 AN: 2116

Alfa AF: 0.867 Hom.: 49304

Bravo AF: 0.894

Asia WGS AF: 0.963 AC: 3346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.47
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6082527; hg19: chr20-2236775;