20-7113491-A-G

Variant names:

• chr20-7113491-A-G
• rs232659
• ENST00000425900.1:n.82-32866A>G

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-32866A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,704 control chromosomes in the GnomAD database, including 17,372 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 0.44 (17372 hom., cov: 30)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 1 publications found

Genes affected

ENSG00000232271 (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 (AFR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425900.1. 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
	ENSG00000232271	ENST00000425900.1	TSL:2	n.82-32866A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65962 AN: 151590 Hom.: 17323 Cov.: 30

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.436 AC: 66069 AN: 151704 Hom.: 17372 Cov.: 30 AF XY: 0.431 AC XY: 31987 AN XY: 74130

African (AFR) AF: 0.737 AC: 30415 AN: 41274

American (AMR) AF: 0.456 AC: 6942 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3468

East Asian (EAS) AF: 0.507 AC: 2614 AN: 5154

South Asian (SAS) AF: 0.255 AC: 1228 AN: 4816

European-Finnish (FIN) AF: 0.262 AC: 2767 AN: 10548

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19703 AN: 67914

Other (OTH) AF: 0.421 AC: 889 AN: 2110

Alfa AF: 0.354 Hom.: 1405

Bravo AF: 0.469

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.57
PhyloP100		0.091

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs232659;

hg19: chr20-7094138;