rs889014

chr5-173557111-C-T

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 0.416 in 151,978 control chromosomes in the GnomAD database, including 13,941 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 0.42 (13941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

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 = 0.548 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: 0.415 AC: 63076 AN: 151860 Hom.: 13910 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.416 AC: 63169 AN: 151978 Hom.: 13941 Cov.: 32 AF XY: 0.415 AC XY: 30855 AN XY: 74276

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.435

Alfa AF: 0.361 Hom.: 19195

Bravo AF: 0.420

Asia WGS AF: 0.321 AC: 1119 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	0.87
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs889014; hg19: chr5-172984114; COSMIC: COSV60233201;