rs11725593

Variant names:

• chr4-27064416-G-A
• rs11725593

Your query was ambiguous. Multiple possible variants found:

• chr4-27064416-G-A
• chr4-27064416-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 0.259 in 152,038 control chromosomes in the GnomAD database, including 5,641 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 0.26 (5641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 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: 0.259 AC: 39379 AN: 151918 Hom.: 5645 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.259 AC: 39370 AN: 152038 Hom.: 5641 Cov.: 32 AF XY: 0.256 AC XY: 19032 AN XY: 74318

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.313

Alfa AF: 0.296 Hom.: 2760

Bravo AF: 0.257

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11725593; hg19: chr4-27066038;