rs6082527

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-2256129-G-A
• chr20-2256129-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000286022 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000286022	ENST00000651531.1	c.-48-1825G>A		intron_variant	Intron 1 of 13			ENSP00000498584.1

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

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.876

Alfa AF: 0.853 Hom.: 24978

Bravo AF: 0.894

Asia WGS AF: 0.963 AC: 3346 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	0.23
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6082527; hg19: chr20-2236775;