rs715260

Variant names:

• chr4-10126522-C-G
• rs715260

Your query was ambiguous. Multiple possible variants found:

• chr4-10126522-C-G
• chr4-10126522-C-T

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 0.248 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
• Publications: 6 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.250 AC: 10391 AN: 41498

American (AMR) AF: 0.205 AC: 3132 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3464

East Asian (EAS) AF: 0.146 AC: 753 AN: 5174

South Asian (SAS) AF: 0.174 AC: 838 AN: 4824

European-Finnish (FIN) AF: 0.238 AC: 2517 AN: 10578

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17836 AN: 67968

Other (OTH) AF: 0.266 AC: 561 AN: 2110

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs715260; hg19: chr4-10128146;