rs171821

Variant names:

• chr5-80401391-T-C
• rs171821

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 0.235 in 152,180 control chromosomes in the GnomAD database, including 7,895 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 0.24 (7895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.583 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: 0.235 AC: 35672 AN: 152060 Hom.: 7854 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.235 AC: 35775 AN: 152180 Hom.: 7895 Cov.: 32 AF XY: 0.233 AC XY: 17311 AN XY: 74418

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.0732

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0917

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.212

Alfa AF: 0.155 Hom.: 746

Bravo AF: 0.253

Asia WGS AF: 0.163 AC: 567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.21
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs171821; hg19: chr5-79697210;