rs316414

chr5-43004178-A-G

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 0.668 in 152,090 control chromosomes in the GnomAD database, including 34,561 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 0.67 (34561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

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 = 0.738 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: 0.668 AC: 101518 AN: 151972 Hom.: 34520 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.668 AC: 101608 AN: 152090 Hom.: 34561 Cov.: 32 AF XY: 0.661 AC XY: 49139 AN XY: 74352

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.674

Alfa AF: 0.646 Hom.: 5459

Bravo AF: 0.660

Asia WGS AF: 0.512 AC: 1778 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	1.9
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs316414; hg19: chr5-43004280;