rs261360

Variant names:

• chr20-5057128-G-A
• rs261360

Your query was ambiguous. Multiple possible variants found:

• chr20-5057128-G-A
• chr20-5057128-G-C
• chr20-5057128-G-T

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 0.381 in 151,910 control chromosomes in the GnomAD database, including 11,360 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 (11360 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 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: 0.382 AC: 57919 AN: 151792 Hom.: 11357 Cov.: 31

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.381 AC: 57941 AN: 151910 Hom.: 11360 Cov.: 31 AF XY: 0.383 AC XY: 28459 AN XY: 74230

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.525

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.361

Alfa AF: 0.365 Hom.: 23561

Bravo AF: 0.371

Asia WGS AF: 0.289 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
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: rs261360; hg19: chr20-5037774;