rs2426515

Variant names:

• chr20-54456178-T-C
• rs2426515

Your query was ambiguous. Multiple possible variants found:

• chr20-54456178-T-C
• chr20-54456178-T-G

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 0.383 in 152,050 control chromosomes in the GnomAD database, including 17,464 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 0.38 (17464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.383 AC: 58155 AN: 151932 Hom.: 17404 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.383 AC: 58284 AN: 152050 Hom.: 17464 Cov.: 31 AF XY: 0.370 AC XY: 27533 AN XY: 74332

African (AFR) AF: 0.840 AC: 34819 AN: 41436

American (AMR) AF: 0.284 AC: 4332 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3462

East Asian (EAS) AF: 0.191 AC: 990 AN: 5172

South Asian (SAS) AF: 0.111 AC: 534 AN: 4826

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10592

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14449 AN: 67968

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.170 Hom.: 524

Bravo AF: 0.420

Asia WGS AF: 0.197 AC: 689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2426515; hg19: chr20-53072717;