rs2419914

Positions:

• chr5-158417878-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 0.481 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;