rs2423311

Variant names:

• chr20-7853590-T-C
• rs2423311

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 0.301 in 151,876 control chromosomes in the GnomAD database, including 7,301 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 0.30 (7301 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• 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 (SAS) allele frequency at 95% confidence interval = 0.47 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: 0.301 AC: 45610 AN: 151760 Hom.: 7281 Cov.: 31

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.301 AC: 45677 AN: 151876 Hom.: 7301 Cov.: 31 AF XY: 0.300 AC XY: 22239 AN XY: 74230

African (AFR) AF: 0.378 AC: 15667 AN: 41402

American (AMR) AF: 0.311 AC: 4747 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1174 AN: 3466

East Asian (EAS) AF: 0.324 AC: 1668 AN: 5142

South Asian (SAS) AF: 0.487 AC: 2338 AN: 4802

European-Finnish (FIN) AF: 0.205 AC: 2162 AN: 10560

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16898 AN: 67948

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.264 Hom.: 2413

Bravo AF: 0.311

Asia WGS AF: 0.447 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2423311; hg19: chr20-7834237;