rs4757245

chr11-14276326-A-Cchr11-14276326-A-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 0.268 in 151,408 control chromosomes in the GnomAD database, including 6,125 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 0.27 (6125 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 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: 0.268 AC: 40534 AN: 151290 Hom.: 6123 Cov.: 29

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.268 AC: 40559 AN: 151408 Hom.: 6125 Cov.: 29 AF XY: 0.274 AC XY: 20223 AN XY: 73906

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.268

Alfa AF: 0.321 Hom.: 7772

Bravo AF: 0.253

Asia WGS AF: 0.329 AC: 1147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.40
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4757245; hg19: chr11-14297872;