rs4901519

Variant names:

• chr14-54552462-A-C
• rs4901519

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 0.194 in 151,892 control chromosomes in the GnomAD database, including 3,388 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 0.19 (3388 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.364 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: 0.193 AC: 29364 AN: 151776 Hom.: 3377 Cov.: 31

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.0866

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.194 AC: 29411 AN: 151892 Hom.: 3388 Cov.: 31 AF XY: 0.192 AC XY: 14233 AN XY: 74280

African (AFR) AF: 0.298 AC: 12323 AN: 41374

American (AMR) AF: 0.182 AC: 2779 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 393 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1951 AN: 5160

South Asian (SAS) AF: 0.255 AC: 1229 AN: 4820

European-Finnish (FIN) AF: 0.0866 AC: 912 AN: 10530

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9298 AN: 67944

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.153 Hom.: 1014

Bravo AF: 0.205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.42
DANN	Benign	0.14
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4901519; hg19: chr14-55019180;