chr11-14276326-A-C

Variant names:

• chr11-14276326-A-C
• rs4757245

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 0.268 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
• Publications: 9 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.117 AC: 4842 AN: 41336

American (AMR) AF: 0.258 AC: 3917 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1344 AN: 3456

East Asian (EAS) AF: 0.373 AC: 1876 AN: 5030

South Asian (SAS) AF: 0.367 AC: 1750 AN: 4772

European-Finnish (FIN) AF: 0.369 AC: 3861 AN: 10464

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22024 AN: 67866

Other (OTH) AF: 0.268 AC: 561 AN: 2096

Alfa AF: 0.300 Hom.: 15227

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
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs4757245; hg19: chr11-14297872;