rs2419914

Variant names:

• chr5-158417878-G-A
• rs2419914

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 0.481 in 151,894 control chromosomes in the GnomAD database, including 18,272 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 0.48 (18272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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: 0.480 AC: 72918 AN: 151776 Hom.: 18234 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.481 AC: 73006 AN: 151894 Hom.: 18272 Cov.: 32 AF XY: 0.475 AC XY: 35245 AN XY: 74236

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.512

Alfa AF: 0.467 Hom.: 2135

Bravo AF: 0.480

Asia WGS AF: 0.419 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419914; hg19: chr5-157844886;