rs1954548

chr14-57177800-G-A

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 0.0949 in 152,200 control chromosomes in the GnomAD database, including 1,516 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 0.095 (1516 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.799

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.0948 AC: 14413 AN: 152082 Hom.: 1513 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0437

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0144

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.0949 AC: 14440 AN: 152200 Hom.: 1516 Cov.: 33 AF XY: 0.0931 AC XY: 6928 AN XY: 74428

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0208

Gnomad4 EAS AF: 0.0922

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0144

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0507 Hom.: 115

Bravo AF: 0.105

Asia WGS AF: 0.0650 AC: 227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	6.5
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1954548; hg19: chr14-57644518;