20-7082489-A-G

Variant names:

• chr20-7082489-A-G
• rs1157366
• ENST00000425900.1:n.81+12795A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000425900.1(ENSG00000232271):​n.81+12795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.065 in 151,888 control chromosomes in the GnomAD database, including 423 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 0.065 (423 hom., cov: 32)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

ENSG00000232271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0854 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
ENSG00000232271	ENST00000425900.1	n.81+12795A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0651 AC: 9882 AN: 151770 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0718

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

GnomAD4 genome AF: 0.0650 AC: 9877 AN: 151888 Hom.: 423 Cov.: 32 AF XY: 0.0664 AC XY: 4927 AN XY: 74246

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0752

Gnomad4 ASJ AF: 0.0878

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0672

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0174 Hom.: 267

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1157366; hg19: chr20-7063136;