rs697550

Variant names:

• chr5-14072344-T-G
• rs697550

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 0.217 in 151,992 control chromosomes in the GnomAD database, including 4,828 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 0.22 (4828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 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: 0.217 AC: 32893 AN: 151874 Hom.: 4812 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0506

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.217 AC: 32977 AN: 151992 Hom.: 4828 Cov.: 32 AF XY: 0.214 AC XY: 15912 AN XY: 74292

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0509

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.174

Alfa AF: 0.152 Hom.: 2876

Bravo AF: 0.224

Asia WGS AF: 0.205 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs697550; hg19: chr5-14072453;