14-57998268-G-C

Variant names:

• chr14-57998268-G-C
• rs2747100

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 0.512 in 151,914 control chromosomes in the GnomAD database, including 20,105 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 0.51 (20105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.914
• Publications: 3 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 = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77745 AN: 151796 Hom.: 20071 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.512 AC: 77837 AN: 151914 Hom.: 20105 Cov.: 32 AF XY: 0.512 AC XY: 37970 AN XY: 74228

African (AFR) AF: 0.481 AC: 19921 AN: 41402

American (AMR) AF: 0.502 AC: 7658 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1675 AN: 3466

East Asian (EAS) AF: 0.647 AC: 3342 AN: 5164

South Asian (SAS) AF: 0.433 AC: 2081 AN: 4806

European-Finnish (FIN) AF: 0.535 AC: 5637 AN: 10538

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35951 AN: 67956

Other (OTH) AF: 0.495 AC: 1045 AN: 2110

Alfa AF: 0.520 Hom.: 2456

Bravo AF: 0.509

Asia WGS AF: 0.536 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.62
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2747100; hg19: chr14-58464986;