rs986217

Variant names:

• chr5-71448831-A-C
• rs986217

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 0.413 in 152,032 control chromosomes in the GnomAD database, including 13,371 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 0.41 (13371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.46 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: 0.413 AC: 62773 AN: 151914 Hom.: 13373 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.413 AC: 62794 AN: 152032 Hom.: 13371 Cov.: 32 AF XY: 0.414 AC XY: 30787 AN XY: 74328

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.459

Gnomad4 OTH AF: 0.419

Alfa AF: 0.427 Hom.: 1325

Bravo AF: 0.393

Asia WGS AF: 0.406 AC: 1414 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs986217; hg19: chr5-70744658;