rs10520889

Variant names:

• chr5-23280811-T-C
• rs10520889

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 0.179 in 151,510 control chromosomes in the GnomAD database, including 2,674 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 0.18 (2674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.19
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.353 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: 0.179 AC: 27075 AN: 151392 Hom.: 2653 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.179 AC: 27135 AN: 151510 Hom.: 2674 Cov.: 32 AF XY: 0.182 AC XY: 13486 AN XY: 74036

African (AFR) AF: 0.231 AC: 9545 AN: 41406

American (AMR) AF: 0.191 AC: 2895 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 632 AN: 3458

East Asian (EAS) AF: 0.218 AC: 1123 AN: 5152

South Asian (SAS) AF: 0.367 AC: 1768 AN: 4818

European-Finnish (FIN) AF: 0.148 AC: 1568 AN: 10568

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9100 AN: 67626

Other (OTH) AF: 0.200 AC: 419 AN: 2100

Alfa AF: 0.153 Hom.: 5220

Bravo AF: 0.181

Asia WGS AF: 0.316 AC: 1098 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.56
PhyloP100		-5.2

Splicing

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

Other links and lift over

dbSNP: rs10520889; hg19: chr5-23280920;