rs2427400

Variant names:

• chr20-62704323-C-A
• rs2427400

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 0.154 in 152,216 control chromosomes in the GnomAD database, including 1,986 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 0.15 (1986 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.154 AC: 23474 AN: 152098 Hom.: 1987 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.154 AC: 23479 AN: 152216 Hom.: 1986 Cov.: 33 AF XY: 0.157 AC XY: 11653 AN XY: 74422

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.136

Alfa AF: 0.160 Hom.: 378

Bravo AF: 0.141

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2427400; hg19: chr20-61335675;