rs715260

Positions:

• chr4-10126522-C-G
• chr4-10126522-C-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 0.248 in 152,120 control chromosomes in the GnomAD database, including 4,829 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 0.25 (4829 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.997

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.248 AC: 37625 AN: 152004 Hom.: 4819 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.248 AC: 37664 AN: 152120 Hom.: 4829 Cov.: 33 AF XY: 0.243 AC XY: 18081 AN XY: 74366

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.266

Alfa AF: 0.123 Hom.: 215

Bravo AF: 0.248

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.054
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs715260; hg19: chr4-10128146;