chr14-55733755-C-G

Variant names:

• chr14-55733755-C-G
• rs945270

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 0.558 in 152,112 control chromosomes in the GnomAD database, including 26,241 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 0.56 (26241 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 29 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.557 AC: 84685 AN: 151994 Hom.: 26179 Cov.: 33

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.558 AC: 84807 AN: 152112 Hom.: 26241 Cov.: 33 AF XY: 0.555 AC XY: 41284 AN XY: 74354

African (AFR) AF: 0.828 AC: 34382 AN: 41520

American (AMR) AF: 0.545 AC: 8332 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1390 AN: 3470

East Asian (EAS) AF: 0.776 AC: 4019 AN: 5180

South Asian (SAS) AF: 0.568 AC: 2735 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3787 AN: 10576

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.419 AC: 28459 AN: 67954

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.483 Hom.: 2379

Bravo AF: 0.586

Asia WGS AF: 0.627 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.47
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs945270; hg19: chr14-56200473;