rs10520420

Variant names:

• chr4-179218025-T-C
• rs10520420

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0444 in 152,292 control chromosomes in the GnomAD database, including 595 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 0.044 (595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 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: 0.0443 AC: 6744 AN: 152174 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0161

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0444 AC: 6762 AN: 152292 Hom.: 595 Cov.: 32 AF XY: 0.0523 AC XY: 3898 AN XY: 74468

Gnomad4 AFR AF: 0.00483

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0161

Gnomad4 OTH AF: 0.0460

Alfa AF: 0.0273 Hom.: 23

Bravo AF: 0.0465

Asia WGS AF: 0.213 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.46
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520420; hg19: chr4-180139179;