rs10520200

Variant names:

• chr4-171183298-T-G
• rs10520200

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0274 in 152,286 control chromosomes in the GnomAD database, including 82 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 0.027 (82 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0274 (4178/152286) while in subpopulation NFE AF = 0.0458 (3112/68008). AF 95% confidence interval is 0.0444. There are 82 homozygotes in GnomAd4. There are 1911 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 82 gene

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: 0.0274 AC: 4177 AN: 152168 Hom.: 82 Cov.: 31

Gnomad AFR AF: 0.00755

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0457

Gnomad OTH AF: 0.0325

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

GnomAD4 genome AF: 0.0274 AC: 4178 AN: 152286 Hom.: 82 Cov.: 31 AF XY: 0.0257 AC XY: 1911 AN XY: 74464

African (AFR) AF: 0.00753 AC: 313 AN: 41574

American (AMR) AF: 0.0264 AC: 404 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00835 AC: 29 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.00104 AC: 5 AN: 4826

European-Finnish (FIN) AF: 0.0223 AC: 237 AN: 10620

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0458 AC: 3112 AN: 68008

Other (OTH) AF: 0.0322 AC: 68 AN: 2114

Alfa AF: 0.0365 Hom.: 20

Bravo AF: 0.0267

Asia WGS AF: 0.00376 AC: 13 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.36
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs10520200; hg19: chr4-172104449;