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. The variant received -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
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.388 AC: 16053 AN: 41408

American (AMR) AF: 0.338 AC: 5162 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 852 AN: 3460

East Asian (EAS) AF: 0.366 AC: 1892 AN: 5164

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5537 AN: 10552

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26094 AN: 67940

Other (OTH) AF: 0.361 AC: 762 AN: 2108

Alfa AF: 0.368 Hom.: 37782

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
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs261360; hg19: chr20-5037774;