rs872411

Variant names:

• chr5-116725686-C-T
• rs872411

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 0.286 in 151,898 control chromosomes in the GnomAD database, including 6,387 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 0.29 (6387 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

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 (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.286 AC: 43386 AN: 151780 Hom.: 6382 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.286 AC: 43419 AN: 151898 Hom.: 6387 Cov.: 31 AF XY: 0.292 AC XY: 21641 AN XY: 74204

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.283

Alfa AF: 0.266 Hom.: 1373

Bravo AF: 0.279

Asia WGS AF: 0.352 AC: 1224 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	0.37
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: rs872411; hg19: chr5-116061382;