rs1950202

chr14-54373178-G-Achr14-54373178-G-C

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 0.351 in 148,614 control chromosomes in the GnomAD database, including 9,545 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 0.35 (9545 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 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: 0.351 AC: 52185 AN: 148498 Hom.: 9543 Cov.: 27

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.351 AC: 52224 AN: 148614 Hom.: 9545 Cov.: 27 AF XY: 0.350 AC XY: 25277 AN XY: 72300

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.351

Alfa AF: 0.321 Hom.: 11357

Bravo AF: 0.349

Asia WGS AF: 0.432 AC: 1496 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	7.8
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1950202; hg19: chr14-54839896;