20-7396025-G-A

Variant names:

• chr20-7396025-G-A
• rs2423243

Variant summary

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

The variant allele was found at a frequency of 0.202 in 151,936 control chromosomes in the GnomAD database, including 3,592 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 0.20 (3592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 2 publications found

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 (AFR) allele frequency at 95% confidence interval = 0.312 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

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30671 AN: 151818 Hom.: 3576 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.202 AC: 30710 AN: 151936 Hom.: 3592 Cov.: 32 AF XY: 0.205 AC XY: 15227 AN XY: 74250

African (AFR) AF: 0.316 AC: 13093 AN: 41392

American (AMR) AF: 0.215 AC: 3275 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5154

South Asian (SAS) AF: 0.274 AC: 1323 AN: 4824

European-Finnish (FIN) AF: 0.147 AC: 1561 AN: 10586

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9124 AN: 67952

Other (OTH) AF: 0.185 AC: 390 AN: 2110

Alfa AF: 0.156 Hom.: 3309

Bravo AF: 0.211

Asia WGS AF: 0.266 AC: 925 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.36
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2423243; hg19: chr20-7376672;