rs10520440

Variant names:

• chr4-179877852-G-T
• rs10520440

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 0.286 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.100 AC: 4147 AN: 41446

American (AMR) AF: 0.427 AC: 6519 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3468

East Asian (EAS) AF: 0.149 AC: 770 AN: 5154

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4816

European-Finnish (FIN) AF: 0.382 AC: 4021 AN: 10528

Middle Eastern (MID) AF: 0.302 AC: 87 AN: 288

European-Non Finnish (NFE) AF: 0.363 AC: 24694 AN: 67948

Other (OTH) AF: 0.280 AC: 588 AN: 2098

Alfa AF: 0.341 Hom.: 16619

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
PhyloP100		0.0060

Splicing

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

Other links and lift over

dbSNP: rs10520440; hg19: chr4-180799005;