rs2423161

Variant names:

• chr20-6529233-A-C
• rs2423161

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 0.156 in 152,172 control chromosomes in the GnomAD database, including 2,449 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 0.16 (2449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 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: 0.156 AC: 23655 AN: 152054 Hom.: 2431 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00750

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.156 AC: 23713 AN: 152172 Hom.: 2449 Cov.: 32 AF XY: 0.151 AC XY: 11215 AN XY: 74422

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.00732

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.176

Alfa AF: 0.129 Hom.: 781

Bravo AF: 0.165

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2423161; hg19: chr20-6509880;