rs10520440

Positions:

• chr4-179877852-G-T

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 0.286 in 151,936 control chromosomes in the GnomAD database, including 7,394 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 0.29 (7394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

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: 0.286 AC: 43454 AN: 151814 Hom.: 7392 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.286 AC: 43460 AN: 151936 Hom.: 7394 Cov.: 32 AF XY: 0.289 AC XY: 21441 AN XY: 74252

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.280

Alfa AF: 0.344 Hom.: 12464

Bravo AF: 0.282

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520440; hg19: chr4-180799005;