rs1858597

Variant names:

• chr20-167044-A-C
• rs1858597

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 0.362 in 152,088 control chromosomes in the GnomAD database, including 10,363 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 0.36 (10363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 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: 0.362 AC: 54988 AN: 151972 Hom.: 10370 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.362 AC: 54984 AN: 152088 Hom.: 10363 Cov.: 32 AF XY: 0.366 AC XY: 27195 AN XY: 74342

African (AFR) AF: 0.283 AC: 11722 AN: 41478

American (AMR) AF: 0.378 AC: 5779 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1329 AN: 3462

East Asian (EAS) AF: 0.554 AC: 2864 AN: 5172

South Asian (SAS) AF: 0.460 AC: 2217 AN: 4822

European-Finnish (FIN) AF: 0.424 AC: 4476 AN: 10568

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.375 AC: 25496 AN: 67980

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.365 Hom.: 2177

Bravo AF: 0.355

Asia WGS AF: 0.428 AC: 1486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.12
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1858597; hg19: chr20-147685;