rs1951867

Variant names:

• chr14-53940474-G-C
• rs1951867

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 0.06 in 152,212 control chromosomes in the GnomAD database, including 342 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 0.060 (342 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0921 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: 0.0600 AC: 9121 AN: 152094 Hom.: 341 Cov.: 33

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.0749

Gnomad EAS AF: 0.0849

Gnomad SAS AF: 0.0394

Gnomad FIN AF: 0.0358

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0600 AC: 9137 AN: 152212 Hom.: 342 Cov.: 33 AF XY: 0.0585 AC XY: 4352 AN XY: 74412

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.0749

Gnomad4 EAS AF: 0.0843

Gnomad4 SAS AF: 0.0395

Gnomad4 FIN AF: 0.0358

Gnomad4 NFE AF: 0.0451

Gnomad4 OTH AF: 0.0742

Alfa AF: 0.0539 Hom.: 34

Bravo AF: 0.0644

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1951867; hg19: chr14-54407192;