rs927103

Variant names:

• chr20-5298689-G-C
• rs927103

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 0.73 in 151,654 control chromosomes in the GnomAD database, including 40,411 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 0.73 (40411 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.749 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: 0.730 AC: 110655 AN: 151536 Hom.: 40368 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110748 AN: 151654 Hom.: 40411 Cov.: 33 AF XY: 0.732 AC XY: 54226 AN XY: 74092

African (AFR) AF: 0.686 AC: 28360 AN: 41330

American (AMR) AF: 0.730 AC: 11126 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2745 AN: 3466

East Asian (EAS) AF: 0.687 AC: 3534 AN: 5144

South Asian (SAS) AF: 0.770 AC: 3708 AN: 4816

European-Finnish (FIN) AF: 0.772 AC: 8119 AN: 10512

Middle Eastern (MID) AF: 0.722 AC: 208 AN: 288

European-Non Finnish (NFE) AF: 0.750 AC: 50859 AN: 67850

Other (OTH) AF: 0.737 AC: 1553 AN: 2108

Alfa AF: 0.735 Hom.: 5110

Bravo AF: 0.727

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs927103; hg19: chr20-5279335;