rs316762

chr5-41716291-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 0.368 in 152,104 control chromosomes in the GnomAD database, including 12,221 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 0.37 (12221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 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: 0.367 AC: 55833 AN: 151984 Hom.: 12192 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.368 AC: 55915 AN: 152104 Hom.: 12221 Cov.: 32 AF XY: 0.367 AC XY: 27302 AN XY: 74336

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.0351

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.375

Alfa AF: 0.302 Hom.: 3973

Bravo AF: 0.379

Asia WGS AF: 0.203 AC: 706 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	1.3
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs316762; hg19: chr5-41716393;