20-7113723-G-A

Variant names:

• chr20-7113723-G-A
• rs232658
• ENST00000425900.1:n.82-32634G>A

Variant summary

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

The ENST00000425900.1(ENSG00000232271):​n.82-32634G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,806 control chromosomes in the GnomAD database, including 14,908 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 0.41 (14908 hom., cov: 31)
• Consequence: ENSG00000232271 ENST00000425900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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.82-32634G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62163 AN: 151686 Hom.: 14869 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.231

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.410 AC: 62265 AN: 151806 Hom.: 14908 Cov.: 31 AF XY: 0.407 AC XY: 30159 AN XY: 74184

African (AFR) AF: 0.663 AC: 27428 AN: 41378

American (AMR) AF: 0.412 AC: 6277 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1187 AN: 3462

East Asian (EAS) AF: 0.505 AC: 2607 AN: 5158

South Asian (SAS) AF: 0.250 AC: 1201 AN: 4804

European-Finnish (FIN) AF: 0.262 AC: 2758 AN: 10524

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19654 AN: 67934

Other (OTH) AF: 0.404 AC: 851 AN: 2108

Alfa AF: 0.306 Hom.: 2483

Bravo AF: 0.436

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.75
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs232658; hg19: chr20-7094370;