rs10520200

chr4-171183298-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 82 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00753

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00104

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0458

Gnomad4 OTH AF: 0.0322

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520200; hg19: chr4-172104449;