chr5-173557111-C-T

Variant names:

• chr5-173557111-C-T
• rs889014

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;