rs159171

Variant names:

• chr5-21186217-T-C
• rs159171

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 0.0644 in 152,050 control chromosomes in the GnomAD database, including 396 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 0.064 (396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0998 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: 0.0644 AC: 9781 AN: 151932 Hom.: 395 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0342

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0644 AC: 9786 AN: 152050 Hom.: 396 Cov.: 32 AF XY: 0.0692 AC XY: 5145 AN XY: 74326

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.0925

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0342

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0484 Hom.: 47

Bravo AF: 0.0592

Asia WGS AF: 0.0970 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs159171; hg19: chr5-21186326;