rs2145231

Variant names:

• chr20-23644910-G-A
• rs2145231

Variant summary

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

The variant allele was found at a frequency of 0.195 in 152,032 control chromosomes in the GnomAD database, including 3,256 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 (3256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.281 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: 0.195 AC: 29633 AN: 151914 Hom.: 3253 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.195 AC: 29651 AN: 152032 Hom.: 3256 Cov.: 32 AF XY: 0.196 AC XY: 14530 AN XY: 74300

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0929

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.173

Alfa AF: 0.170 Hom.: 2067

Bravo AF: 0.188

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2145231; hg19: chr20-23625547;